From Germplasm to Cup: A Comprehensive Review of the Genetic, Environmental, and Postharvest Determinants of Coffee Quality and Their Interactions

Abstract

Premium coffee depends on high-quality beans, influenced by a combination of genetic, environmental, and postharvest factors. This review summarizes the mechanisms underlying coffee bean quality, with an emphasis on the genetic differences between Coffea arabica and Coffea canephora, as well as the integrated roles of environmental conditions, agronomic practices, including nutrient and shade management, and postharvest processing technologies. The allotetraploid genome of C. arabica is influenced by homoeologous exchanges and subgenome-biased expression (such as decreased DXMT activity that reduces caffeine), which contribute to its complex flavor profile. Key lipid metabolism genes, particularly FADS2, play a critical role in regulating lipid metabolism. The effects of altitude (1600–2000 m) and shade influence various metabolic pathways. Cooler temperatures promote sugar accumulation, while excessive shading hinders carbon assimilation and the development of flavor precursors. Postharvest processing significantly influences flavor, where microbial or enzymatic treatments enhance sensory attributes. In addition, methods like natural, washed, or honey processing modulate various nonvolatile compounds, impacting lipid emulsification and aroma retention. Multi-omics analyses suggest that MYB proteins play a key role in regulating pathways involved in caffeine, chlorogenic acids, and terpenes. Effective hermetic packaging prevents oxidation, thereby preserving freshness. Overall, superior coffee quality stems from synergistic interactions across genetic, ecological, agronomic, and processing factors, highlighting the need for the development of an integrated strategy to support the sustainable production of premium coffee.

1. Introduction

Coffee (Coffea spp.) comprises perennial evergreen shrubs or small trees in the family Rubiaceae, encompassing approximately 130 species. Coffee is widely cultivated in tropical and subtropical regions and ranks among the world’s three most important beverage crops, together with tea and cocoa [1]. FAO statistics for 2024 indicate that the world’s coffee harvested area was 12.47757 million hectares, producing 11.284715 million tonnes, with coffee imports valued at US$35.016 billion and exports at US$34.335 billion. Currently, the five leading coffee-producing countries are Brazil, Indonesia, the Central African Republic, Ethiopia, and Colombia. As a globally important crop, its quality directly affects both market value and the long-term sustainability of the industry. Research indicates that a one-point increase in sensory evaluation score for specialty coffee can lead to an approximate 54.6% rise in auction prices [2]. As the world’s largest coffee-producing country, Brazil accounts for 17.4% of its total coffee export volume through specialty coffee, which generates 23.4% of the total export value [3]. A 2021 survey report by the International Trade Centre indicated that specialty coffee accounted for 38% of the U.S. market share. Projections further indicate that by 2030, the global specialty coffee market will reach a value of 120.54 billion USD [4]. The value of specialty coffee is determined by the delicate balance of hundreds of metabolites in coffee beans, including caffeine, chlorogenic acids, lipids, and volatile aromatic compounds. The accumulation of these compounds is influenced by coffee genotype, environment, and postharvest primary processing practices (Figure 1). Therefore, a systematic analysis of the underlying mechanisms spanning genetic regulation, ecological conditions, agronomic practices, such as nutrient and shade management, and postharvest processing technologies is essential for producing premium coffee.

Current research has mainly focused on the effects of individual factors on coffee quality. These include the role of genotype in regulating alkaloid content [5], the impact of altitude on sugar metabolism, and the influence of nutrient management and processing techniques on the accumulation of flavor precursors [6]. However, recent progress in multi-omics technologies has demonstrated that quality formation is essentially a cross-scale cascade process. This process begins with the activation of MYB transcription factor expression in the genome [7]. It is then followed by the accumulation of stress-related metabolites induced by the microclimate [8]. Finally, it culminates in the metabolic restructuring of microbial communities during fermentation [9]. This complex, interactive mechanism has not been systematically integrated, resulting in insufficient theoretical guidance for optimizing agronomy and enhancing post-harvest innovation. For instance, while cultivating plants in the shade can improve the complexity of their flavor, it may also reduce the efficiency of caffeine biosynthesis [10,11]. Furthermore, excessive use of artificial drying techniques can damage the lipid structures within plasma membranes, contributing to the loss of volatile compounds [12]. This study thoroughly examines the factors affecting the production of high-quality green coffee beans (GCBs), including genetic basis, environmental factors, shade management, nutrient application, post-harvest processing, and storage methods. It explores the intricate interplay among these factors, which collectively shape coffee quality, aiming to clarify research priorities and strategic directions for the coffee industry amid rapid global environmental changes.

2. Genetic Mechanisms Regulating Coffee Bean Quality

Genetic factors play a central role in shaping coffee quality, primarily by regulating the expression of genes associated with key metabolites (e.g., lipids and carbohydrates), secondary metabolites (e.g., alkaloids and terpenes), and developmental characteristics. This section examines key genetic dimensions, including the structural organization of the coffee genome, genes governing essential metabolic pathways, and genetic diversity across cultivars.

2.1. The Role of Genomic Structure in Determining Coffee Bean Quality

Coffea arabica L. is an allotetraploid hybrid of C. eugenioides (E-genome) and C. canephora (C-genome) and possesses a dynamic genomic architecture [13]. Chromosome-scale genome assemblies further show that ongoing structural evolution continuously remodels its genetic landscape and bean quality potential, supplying a key source of diversity despite low nucleotide variation [14,15]. The main dynamic involves frequent homoeologous exchange (HE) between subgenomes. These exchanges are non-random, with a clear bias toward acquiring segments from the C. canephora C-subgenome, indicating possible adaptive selection [15]. By modifying gene dosage and regulatory environments, HEs directly affect the expression of pathways related to quality. A key example is the caffeine biosynthetic gene DXMT, where the C-subgenome contains a single broadly expressed copy of DXMT, whereas the E-subgenome has a tandem duplication that is specifically expressed in fruit. This divergence is probably due to structural variation [14]. Additionally, large-scale chromosomal aberrations, such as aneuploidies and copy-number variants, are prevalent. These structural variants serve as an important mechanism for generating phenotypic diversity and may influence metabolic pathways more significantly than single nucleotide polymorphisms in this genetically restricted species [14]. Genomic analyses have reshaped the understanding of the species history, dating the allopolyploidization event to have occurred between 350,000 and 610,000 years ago and revealing ancient bottlenecks. Importantly, they also detected extensive cryptic introgression from related species, especially C. canephora, into many cultivated lines. While such introgression has supplied vital disease resistance loci, it often carries a quality penalty, highlighting a major challenge for breeding [15]. Similarly, Leal et al. [16] and Vidal et al. [17] demonstrated that the formation of the allopolyploid C. arabica involves genomic reorganization events such as homoeologous exchanges and gene silencing, elimination, or conversion. In summary, the quality of coffee beans results from a complex genomic interaction in which hybrid ancestry and biased HEs influence subgenome expression, structural variants generate diversity, and introgression history integrates adaptive and qualitative traits. Therefore, future quality improvements must consider the entire genetic domains.

2.2. Genetic Regulation of Key Quality-Related Compounds

2.2.1. Caffeine Biosynthesis

Caffeine comprises about 0.85–1.15% of the dry weight of the coffee bean and is synthesized through sequential methylations catalyzed by three SAM-dependent N-methyltransferases: XMT, MXMT, and DXMT [18,19]. The higher caffeine levels in C. canephora (Robusta) compared to C. arabica (Arabica) are attributed to differences in gene copy number, gene expression, and enzyme structure. Robusta possesses three key genes (CcXMT1, CcMXMT1, CcDXMT) that are highly expressed in young tissues. In contrast, Arabica has six homologous genes inherited from its two subgenomes, with generally lower overall expression, particularly from the copies derived from eugenioides [20]. Structural variations, such as Ser-316 in XMT and His-160 in DXMT, are suggested to improve catalytic efficiency in Robusta, but their functional effects remain under debate [21]. Reports on enzyme multifunctionality and substrate specificity remain inconsistent, underscoring the complexity of explaining interspecies differences. For example, some studies suggest that coffee MXMT catalyzes only 3 N methylation, whereas others have reported both 3 N and 1 N methylation activities in specific isoenzymes [20,21]. These discrepancies could stem from variations in experimental systems, such as recombinant versus native enzymes, the plant developmental stage, or the genetic background of the materials. Future research involving near-isogenic lines, controlled physiological environments, and comparative analyses of orthologous isoenzymes will aid in clarifying how gene expression, protein structure, and post-transcriptional regulation each contribute to caffeine biosynthesis.

2.2.2. Lipid Biosynthesis

Lipids represent one of the major compounds in GCBs, accounting for approximately 7–17% of the beans’ dry weight [22]. Coffee lipids mainly consist of triacylglycerols, diterpenes, sterols, and tocopherols. Diterpene compounds, specifically cafestol and kahweol, comprise about 20% of the total lipids [23]. Biosynthesis is regulated across the developmental stages, and transcriptomic data indicate that the early green bean stage is crucial for triacylglycerol and fatty acid synthesis, involving genes including TAG synthase, ω-6 desaturase, and lipid transfer proteins [24]. At the same time, biochemical profiling shows different accumulation patterns for diterpenes, where cafestol primarily accumulates in floral tissues, while kahweol levels rise during fruit development, reaching their maximum in the pericarp at 120 days after flowering [25]. This spatio-temporal divergence suggests specialized and possibly sequential pathways. Genetic research supports this variation. Genome-wide association studies in wild C. arabica populations link lipid content to specific loci, including Cc08_g10680, which encodes a fatty acid desaturase involved in diterpene metabolism [26]. Interspecies comparisons further highlight genetic control, with lipid content differing by over 30% between C. arabica and C. canephora [26]. Additionally, several acyltransferase and phosphatidic acid phosphatase genes have been recognized as central regulators [27]. Our review indicates that variations in sampling design and environmental conditions across earlier studies likely led to differing results. For example, Vamoto et al. [25] focused on quantifying cafestol and kahweol in various coffee organs such as leaves, roots, flowers, and fruits, as well as different tissues within the fruit. In contrast, Sant’Ana et al. [26] primarily analyzed processed coffee beans. Vamoto et al. [25] defined developmental stages based on days after flowering (DAF), whereas Cheng et al. [24] categorized beans into three relative stages: “green,” “yellow,” and “red” for transcriptome analysis. Additionally, storage conditions like temperature, humidity, and oxygen levels can significantly affect lipid composition [23]. Additionally, there is limited functional validation of candidate genes, particularly cytochrome P450s such as CYP76C4 and CYP701A3, which show a link between their expression and diterpene accumulation. [25]. Future research should focus on functional studies and comparative analyses involving different genotypes to better understand regulatory mechanisms to facilitate targeted breeding for lipid-related traits.

2.2.3. Molecular Networks Governing Chlorogenic Acid Synthesis

Chlorogenic acids (CGAs) are the main polyphenols found in green coffee beans, created by esterifying quinic acid with trans-cinnamic acids such as caffeic, ferulic, and p-coumaric acids. The primary classes of CGAs in green coffee include caffeoylquinic acids (CQAs), dicaffeoylquinic acids (diCQAs), and feruloylquinic acids (FQAs), each with several isomers. Among these, 5-caffeoylquinic acid is the most prevalent [28,29,30]. The composition of these compounds directly affects coffee bitterness, acidity, and antioxidant activity [31]. CGA biosynthesis is thought to be co-regulated by the phenylpropanoid and shikimate pathways [32], with key enzymes such as phenylalanine ammonia-lyase (PAL), hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT), and hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) [33]. Although C. arabica and C. canephora show no significant differences in the expression of core genes such as PAL and HCT [34], they exhibit clear interspecific divergence in CGA accumulation, with higher CGA content per fruit in C. canephora (16.9 mg) than in C. arabica (13.6 mg) [29]. This difference could indicate variations in how carbon flux is allocated, with C. arabica showing higher levels of sucrose-phosphate synthase (SPS) and an invertase inhibitor (InvI3), which promotes sucrose accumulation (7.3 to 11.4%). In contrast, increased sucrose breakdown in C. canephora might supply more precursors for CGA biosynthesis [34].

CGA accumulation and composition are complex and dynamically regulated by many factors, which may explain why different studies produce inconsistent results. Firstly, genetic and species differences are key drivers. Wild C. canephora germplasm shows significantly more diversity in CGA isomers (such as 3-CQA and 5-FQA) compared to C. arabica. Additionally, geographic origin, like West versus Central African accessions, greatly influences isomer ratios, suggesting that local adaptation influences CGA metabolism [35]. Secondly, the developmental stage and environment are crucial factors. In C. pseudozanguebariae, total CGAs decrease as the fruit matures, while CQAs rise sharply during late stages, indicating a shift in regulation during development [36]. Temperature plays a key role, as warmer conditions increase the expression of phenylpropanoid pathway genes (PAL2, C4H) and accelerate early 5-CQA accumulation in C. arabica. Conversely, cooler climates delay the peak of accumulation and favor late-stage isomerization toward less common CQA derivatives [37]. This temperature-dependent regulation of transcription may explain regional variations in coffee CGA profiles. Moreover, interannual climatic variability can substantially alter CGA levels within the same cultivar [28], indicating that assessments conducted under a single environmental condition may not fully capture genetic potential.

Overall, the CGA biosynthetic network is a dynamic system regulated across multiple levels. Discrepancies among studies often arise from differences in genetic materials, developmental stages, environmental conditions, and methodologies. Future work should employ multifactorial controlled experiments and integrate transcriptomic and metabolomic analyses to systematically identify key regulatory nodes. In addition, interactions between CGA metabolism and other pathways (such as lignin biosynthesis and sucrose metabolism) should be examined to provide a theoretical basis for breeding coffee cultivars with both desirable flavor and improved health benefits.

Genetic differences in coffee quality traits result from species evolution, changes in metabolic pathways, and epigenetic regulation. Using these mechanisms, molecular markers can be created from structural variants and expression differences in XMT and DXMT to help select for low-caffeine varieties and cultivars. In parallel, targeting CGA biosynthesis genes (e.g., PAL, HCT, and HQT) and upstream sucrose metabolism genes (e.g., SPS) may enable breeding high CGA cultivars to enhance antioxidant capacity and improve flavor balance. Recent advances in coffee genomics have made flavor-oriented breeding increasingly feasible, supporting integrated strategies that combine disease resistance, quality, and climate adaptation [15,38]. This approach may overcome limitations of traditional phenotype-based selection, which typically requires 10 to 20 years per generation and is increasingly misaligned with market-driven breeding cycles. However, significant challenges still exist in improving coffee quality through genetic methods. The intricate allopolyploid genome of Arabica coffee makes it difficult to validate the functions of candidate genes. Although progress has been made in understanding its genome structure and identifying key metabolic pathways, the precise mechanisms by which gene expression influences the production of major chemical compounds remain unclear. Additionally, coffee aroma development involves many inducible volatile compounds, but the pathways for precursor accumulation, their conversion, and the gene regulatory networks involved have not been thoroughly explored. Future research should focus on understanding the functions of genes involved in lipid- and sugar-based precursor biosynthesis and on examining how their expression differs across coffee species with effect on CGA and processing [39,40]. Future research efforts should focus on: (1) developing haplotype-resolved genomes and pangenomes to better understand complex allelic interactions; (2) combining multiomics data with genetic mapping to identify genome-wide regulatory networks responsible for key quality traits such as chlorogenic acids and caffeine; (3) conducting gene function validation and mechanistic studies, especially in tetraploid backgrounds, to understand how structural variation and gene dosage influence metabolic pathways; and (4) exploring the genetic foundations of aroma precursor biosynthesis and conversion to enable precise flavor engineering.

3. Ecological and Environmental Regulatory Network

As a typical shade-adapted tropical plant, coffee is mainly grown within the “Bean Belt,” which extends between 25° N and 25° S. The unique combination of light, temperature, and water provides the ecological foundation for the synthesis of flavor-related metabolites when coffee is grown in this region [41]. Complex interactions between genotype and various ecological factors, such as temperature, humidity, altitude, and nutrient availability, shape the quality of GCBs. These factors act through interconnected metabolic networks, with regulatory mechanisms exhibiting pronounced spatial and temporal heterogeneity (Figure 2).

3.1. Impact of Temperature

Temperature plays a crucial role in coffee development, metabolic processes, and bean quality. Although optimal temperature ranges are established for key species such as C. canephora (around 30/26 °C day/night), C. eugenioides (23/19 °C), and the hybrid C. arabica (20–24 °C annual average) but there are notable discrepancies among studies concerning exact thermal thresholds during different developmental stages and among various genotypes [42,43,44]. For example, C. arabica is usually considered heat-sensitive; recent studies indicate it can be quite resilient up to 37 °C under controlled environments, especially when combined with elevated CO₂ [45]. This underscores the importance of experimental context, such as irradiance, water availability, and atmospheric CO₂ levels, for interpreting thermal tolerance data.

At the molecular level, C. arabica under heat stress exhibits widespread changes in gene expression, yet homeolog expression ratios remain largely stable (r = 0.06, p < 0.001), implying that polyploid regulatory networks, rather than subgenome-specific reprogramming, underpin thermal adaptation [42,46]. This genomic plasticity could account for the higher heat tolerance observed in wild relatives such as C. racemosa, which activates a multi-layered defense mechanism involving receptor-like kinases, calcium/MAPK pathways, and WRKY-driven increase in HSPs and antioxidant gene expression. [47]. HSPs indeed serve as early thermosensors, with some small HSPs like Cc11_g16360 downregulated under moderate heat (30/26 °C), possibly to stabilize protein folding, while rubisco activase (Cc04_g14500) is upregulated to sustain photosynthesis [48,49,50]. These responses indicate a coordinated trade-off between protecting protein integrity and maintaining carbon assimilation, a balance that might differ across species and various conditions.

Temperature significantly influences both the physiological performance of coffee beans and their composition, thereby affecting beverage quality. Higher temperatures during ripening generally accelerate development and alter metabolic pathways, often leading to lower levels of desirable flavor precursors. For instance, warm climates tend to increase volatile compounds associated with off-flavors, such as earthy and green notes, whereas cooler environments promote acidity and fruity flavors [51]. Specifically, compounds such as butan-2,3-diol and butan-1,3-diol show a positive correlation with heat and negative sensory qualities, whereas ethanol and acetone are linked to cooler conditions and improved cup quality [51]. Additionally, heat stress alters the profile of chlorogenic acid (CGA) isomers: 3-CQA and 4-CQA increase, while 5-CQA decreases, thereby potentially impacting bitterness and antioxidant activity [45,52].

Current research on the effect of temperature on coffee faces several limitations. Differences in heat-tolerance among cultivars and genotypes have not been thoroughly quantified under real-world field conditions. Most studies examine acute heat stress, while the impact of prolonged suboptimal temperatures on coffee flavor chemistry is less explored [42,46,47]. The mechanistic connections between temperature sensing, such as through heat-shock proteins or membrane fluidity, and subsequent metabolic changes in beans are mostly speculative. Although elevated CO₂ appears to reduce heat-stress effects, its long-term impact on crop growth and taste remains unclear [45]. Overall, temperature affects coffee through complex physiological, molecular, and biochemical pathways that are influenced by genetic factors, growth stage, and environmental conditions. Future research should implement a systems approach, combining transcriptomics, metabolomics, and sensory analysis in both the lab and field, to better understand these interactions and aid in developing climate-resilient coffee varieties.

3.2. Impact of Humidity and Rainfall

Humidity and rainfall directly impact coffee bean quality by affecting plant physiology and fruit development. C. arabica generally thrives at around 70% relative humidity and 1500 to 2000 mm of annual rainfall, while C. canephora prefers higher humidity of about 85% and more annual rainfall, between 2000 and 3000 mm [53]. These two species differ markedly in stomatal density, water-use efficiency, and drought tolerance, resulting in distinct responses to vapor pressure deficit (VPD) and drought stress [53,54,55,56]. Rainfall patterns affect bean size and quality: insufficient rainfall late in the season decreases the percentage of large beans, while excessive rainfall at harvest significantly increases the risk of insect damage and fungal contamination [57]. Waterlogging stress hampers photosynthesis, nitrogen uptake, and metabolite assimilation, resulting in lower biomass, increased bean defects, and changes in the biosynthesis of flavor precursors, such as sugars and organic acids [58,59,60,61,62,63].

However, existing findings remain inconsistent. Some studies report that moderate water stress can improve sensory qualities [64,65], whereas field-based controlled experiments conducted by Pappo et al. [66] demonstrated that key sensory attributes such as acidity generally declined despite the increase in yield. Similarly, reported associations between altitude and biochemical constituents (caffeine and trigonelline) are inconsistent across studies [66]. These discrepancies suggest that quality responses are shaped by interactions among cultivar genetic background, stress intensity, local microclimate, and management practices, and that purely descriptive correlations are insufficient to resolve the underlying mechanisms.

Currently, there is limited systematic and quantitative physiological and biochemical evidence to decipher the influence of rainfall on the synthesis and breakdown of specific flavor precursors, like sugars and amino acids. Furthermore, the specific quantitative relationships and molecular mechanisms linking high-humidity environments to pest and disease outbreaks, such as coffee leaf rust, and the resulting decline in crop quality are not well understood. Future research should combine environmental management, multi-omics profiling, and regional comparisons to determine threshold effects and elucidate the mechanistic pathways of major environmental factors. This approach will support adaptive breeding and targeted agronomic practices.

3.3. Effect of Altitude

Altitude shapes coffee quality through complex interactions with environmental factors, genetic makeup, and agronomic practices. Tolessa et al. [67] showed that coffee grown at higher elevations (1950–2100 m) has better bean appearance, aroma, and overall quality than coffee from mid-elevations (1600–1680 m). Still, these general patterns are not consistently observed across studies. For example, Worku et al. reported that caffeine and chlorogenic acid (CGA) content decreased with increasing altitude in Ethiopian plantations [68]. In contrast, Avelino et al. observed the opposite pattern in Costa Rican terroirs [69]. These differences highlight how altitude effects are related to prevailing conditions and can also be influenced by factors such as cultivar genetics, climate, and slope orientation. For example, slope orientation affects morning sunlight exposure and, in turn, impacts coffee acidity [69]. Thus, altitude alone is an insufficient predictor of quality, and its impact must be interpreted within a broader ecological and management context.

The biochemical changes associated with elevation, including lower caffeine and CGA [68,70], higher sucrose and niacin [70], and increased polyphenol biosynthesis, are often linked to cooler temperatures and longer maturation periods [68,71]. Metabolomic analyses show that beans grown at 1600–1800 m can have higher levels of caffeine, CGA-related intermediates, and sucrose metabolites under certain production conditions [72,73]. This trend might be due to higher diurnal temperature swings at higher altitudes, which can boost phenylpropanoid flux by increasing phenylalanine ammonia lyase activity, thereby promoting chlorogenic acid accumulation [71,72,74]. However, these responses are not straightforward because, above 2000 m, ongoing low-temperature stress can trigger bursts of reactive oxygen species (ROS) [72,75], deplete antioxidants, and increase lipid peroxidation [73], ultimately weakening the oxidative stability of coffee beans. Additionally, postharvest processing techniques and shade management can significantly influence the biochemical profiles associated with altitude. Worku et al. [68] showed that wet processing enhances sucrose accumulation at higher altitudes more than dry processing. These interactions demonstrate that biochemical effects are not solely determined by altitude but are also shaped by pre- and postharvest practices.

Desired coffee quality results from balancing altitude with complementary agronomic practices. While elevations around 1900–2000 m typically support better cup qualities, very high altitudes can cause physiological stress and reduce quality. Different C. arabica subspecies or cultivars perform differently along altitudinal gradients, affected by genetic traits involved in flavor precursor production, disease resistance, and environmental adaptability. Future research should go beyond simple altitude-quality correlations and focus on understanding how genotype, microenvironment, and management interact. This will help develop specialized cultivation strategies that enhance quality without relying solely on high-altitude locations.

3.4. Nutrient Regulation and Its Role in Coffee Bean Development

Nutrient management affects crop growth and root nutrient uptake efficiency, which directly impacts coffee yield and quality [76]. During the vegetative growth stage, nitrogen is the most needed nutrient, followed by phosphorus, potassium, calcium, and organic matter [77].

Nitrogen fertilization is vital for coffee development due to supporting photosynthesis, nutrient uptake, and, ultimately, yield. Its highest requirement occurs during fruit expansion, approximately 209–237 days after sowing [78]. However, managing N requires a critical balance, where adequate N boosts production, and application methods significantly influence Nitrogen Use Efficiency (NUE) and environmental effects [79]. Nitrogen tracer experiments show NUE can range from very low (−25%) with high leaching losses in saturated, humid agroforestry systems to over 75% in well-managed monocultures with moderate rainfall [80]. This significant variation is caused not by the crop itself but by key environmental factors such as climate (rainfall and drainage), soil type, N saturation levels, system design (like the presence of shade trees), and the crop’s growth stage—young vegetative plants tend to recover minimally in the short term [77]. Additionally, the nitrogen source greatly impacts bean quality; ammonium-based fertilizers can lead to soil acidification and inhibit flavor enzymes, whereas nitrate sources may enhance aromatic compounds [81]. Consequently, effective N management should involve a tailored, context-specific approach that moves away from uniform high-dose fertilization, aiming to optimize yield, environmental sustainability, and coffee flavor quality.

Potassium is an essential nutrient for coffee quality, affecting biochemical and sensory properties mainly by aiding sugar transport, bean filling, and secondary metabolite production [76]. Although potassium fertilization generally increases lipid and chlorogenic acid levels, its effectiveness depends heavily on irrigation management, with controlled watering crucial to prevent sucrose loss and enhance quality [82]. The type of potassium source also affects quality outcomes through accompanying ions, rather than directly altering key flavor compounds such as caffeine, trigonelline, or 5-CQA [83]. For example, potassium chloride (KCl) often reduces beverage quality because of chloride ion buildup. In contrast, alternative sources such as K₂SO₄ and KNO₃ do not significantly affect major chemical parameters, although they do influence NO₃⁻ and SO₄⁻² levels in beans [83,84]. The effect of potassium sources is often influenced by cultivar-specific responses, such as Aranás, sustain high yields regardless of the potassium source, whereas others, such as Catigua and Topázio, exhibit consistent yield losses, highlighting the importance of genetics in determining yield potential [83]. Variations in the literature regarding the effects of potassium may stem from differences in experimental conditions, including irrigation, soil type, climate, and assessment methods, highlighting the need for context-specific optimization. Consequently, selecting potassium sources for coffee production should consider local growing conditions and cultivar traits to enhance yield and sensory quality effectively.

Regarding the impact of phosphorus fertilization on coffee quality, studies indicate effects vary depending on specific circumstances, warning against broad generalizations. While applying N, P, and K fertilizers at certain growth stages can boost biochemical components like total sugar and chlorogenic acid in beans [76]. Research in high-density planting systems in Brazil’s Zona da Mata found no notable increase in yield or biennial stability from P fertilization over several seasons, even though soil and leaf P levels rose [85]. This indicates that in some soil and farming conditions, especially with sufficient initial fertility, P may not limit coffee yield or quality. Studies in the Cerrado region also found that irrigation practices have a greater effect on soil microbial activity and organic carbon fractions than P-splitting methods, although a single high P dose under irrigation elevated microbial biomass and acid phosphatase activity [86]. Likewise, in controlled irrigation and fertilization experiments, P application had little effect on bean biochemical composition, whereas nitrogen and potassium exerted significant effects [82]. These findings emphasize that environmental factors, soil characteristics, and management practices influence P response, underscoring the need for tailored, site-specific nutrient recommendations rather than one-size-fits-all fertilization plans.

Beyond the primary macronutrients, micronutrients also play critical roles in coffee physiology and show substantial genetic variability, which may indirectly influence bean quality attributes. In Coffea canephora, the concentrations of micronutrients in leaves, flowers, grains, and husk generally follow the order Fe > B > Mn > Cu > Zn, with Fe being the most abundant [87,88]. However, these accumulation patterns vary considerably among genotypes. For example, in a study of 20 C. canephora genotypes, grain Fe concentration ranged from 12.13 to 42.33 mg kg⁻¹, whereas Mn ranged from 14.87 to 23.43 mg kg⁻¹ and B from 5.60 to 15.67 mg kg⁻¹, indicating substantial genetic diversity in micronutrient uptake and allocation. [88]. Similarly, leaf micronutrient concentrations vary across seasons, with Fe and B often peaking during the early growth stages and declining during fruit filling, suggesting active remobilization to developing fruits [89]. This genotype-dependent variation in micronutrient dynamics is further supported by the high heritability estimates reported for several micronutrients, such as Mn in husk (H² = 97.17%) and Cu in grain (H² = 90.25%), indicating strong genetic control and substantial potential for targeted breeding [88]. Although the direct effects of micronutrients on flavor precursors require further investigation, their essential roles in enzyme catalysis, carbohydrate metabolism, and stress responses underscore their importance in comprehensive nutrient management strategies to optimize coffee quality.

The current understanding of nutrient management in coffee has several gaps. Future research should employ more systematic and detailed methods, such as combining multi-environment and multi-genotype interaction experiments, to clarify the molecular and physiological pathways through which nutrients influence quality. Furthermore, developing precision management strategies backed by long-term monitoring and data-driven models can simultaneously improve yield, flavor, and ecological sustainability.

4. Multidimensional Impacts of Shading Systems

Shading plays a crucial role in coffee agroforestry, affecting microclimates, soil, and biological interactions. While its influence on coffee quality is well known, the effects are complex and differ based on the context, involving physiological, biochemical, and ecological factor processes (Figure 3).

Research shows that shading affects coffee quality through several mechanisms, including regulating fruit development, carbohydrate metabolism, and secondary compound biosynthesis. However, effects reported differ widely across studies, highlighting the need to examine the roles of environmental and management factors.

Under moderate shade and less ideal conditions, especially in warmer, lower-altitude areas, shading at 30–50% often enhances cup quality. This improvement is likely due to less heat stress, longer bean development, and increased buildup of sugars and aroma precursors [10,90]. For example, 50% shading has been shown to boost bean size and enzyme activity related to sucrose metabolism, resulting in sweeter cup scores [90]. In southwestern Ethiopia, shade interacts with altitude to affect sucrose levels and acidity [68]. These advantages support the idea that shade helps mitigate excessive temperatures, bringing the microclimate closer to the ideal range for C. arabica. Conversely, research in cooler, high-altitude areas has shown that shade can have neutral or adverse effects on sensory quality. In Southern Colombia, shade negatively impacted fragrance, acidity, body, and preference scores of C. arabica cv. Caturra in the higher-altitude zone of Oporapa, while it had minimal influence in the lower-altitude Timaná [91]. This indicates that in cool environments, additional shading might lower temperatures below optimal levels, hindering metabolic processes vital for quality development [68,91]. Additionally, enhanced shade (>60%) increases competition for resources (light, water, nutrients), significantly reduces flowering and yields [91,92], and can decrease the biosynthesis of compounds like chlorogenic acids by downregulating enzymes such as phenylalanine ammonia-lyase (PAL) [10]. Excessive shade also raises humidity, which can promote diseases like coffee leaf rust (CLR) [93].

C. arabica and C. canephora (Robusta) respond differently to shade. A meta-analysis on Robusta coffee found that shade typically enhances growth and yield, especially in older trees and certain clones like 06V and C153 under moderate shade levels of 41–65% [66]. Nevertheless, higher shade levels (>30%) can negatively impact beverage quality [66]. In contrast, Arabica shows more complex, often altitude-dependent, quality responses.

Despite extensive research, significant gaps still prevent a fully predictive understanding of how shade interacts with quality, which hampers precise agroforestry design aimed at quality improvement.

Mechanistic insights into how shade influences biochemical pathways: Although it is known that shade affects levels of key compounds such as caffeine, chlorogenic acids, and sucrose [68,94], the long-term behaviors and exact molecular mechanisms are not well understood. Future studies should go beyond correlation and explore how light signaling influences gene networks involved in producing secondary metabolites linked to quality [94,95,96]. Employing advanced omics tools (transcriptomics, metabolomics, proteomics) is vital to uncover these pathways and find candidate genes or markers associated with high quality under specific shade conditions [39,97].

Absence of comprehensive models and standard metrics: Data quantifying how shade levels (light, moderate, heavy) precisely control chemical composition are inconsistent and not integrated into predictive models [94]. Developing standardized frameworks to measure shade interactions with local climate factors (temperature, rainfall, vapor pressure deficit), especially across altitude gradients, is essential [68]. Additionally, the combined effects of shade and postharvest processes (e.g., wet vs. dry) on final cup quality need systematic assessment [68].

Necessity for validation in specific contexts and clone selection: The high variability across environments emphasizes the need for multi-location trials testing different shade tree species and coffee genotypes (clones/cultivars) [66]. Identifying which shade tree–coffee combinations work best for particular agro-ecological zones will help guide farmers. For Robusta, clones like 06V and C153 are promising for shaded systems [66,98], while Arabica recommendations should consider altitude and temperature specifics.

In conclusion, the link between shade and coffee quality is not straightforward but is influenced by a complex mix of environmental limits, genetic potential, and management techniques. Future research should focus on mechanistic studies, long-term system analyses, and creating context-specific models to turn ecological complexity into dependable methods for cultivating high-quality coffee within sustainable agroforestry systems.

5. Postharvest Handling and Processing

5.1. The Impact of Primary Processing on Coffee Flavor

Postharvest processing is a critical stage that affects coffee flavor and quality, accounting for roughly 60% of the final cup profile [99]. The traditional primary methods include natural (dry), washed (wet), and honey (semi-dry), and each produces unique sensory characteristics by differently influencing the microbial environment and metabolic activities within coffee beans [100]. These procedures modify the chemical makeup of green coffee beans (GCBs), especially their non-volatile metabolites, which are essential precursors for flavor development during roasting through Maillard reactions, caramelization, and other heat-induced changes [101,102,103,104].

While non-volatile compounds like sugars, amino acids, organic acids, and phenolics primarily shape flavor potential [105,106], recent metabolomic research shows that their buildup depends greatly on processing methods. For instance, in Yunnan C. arabica, sun-dried beans gather more chlorogenic acid analogs, which contribute to bitterness and astringency after roasting. In contrast, washed beans contain higher caffeine levels, boosting bitterness and body [107]. Honey-processed beans contain unique phenolamides, such as N-caffeoyltryptophan, which may confer bioactive benefits and affect astringency. These results highlight that different processing techniques selectively enrich certain metabolites, shaping the sensory profile of roasted coffee.

The connection between processing and flavor is complex, as conflicting findings in the literature imply that other factors strongly interact with processing effects. A comprehensive metabolomic analysis of 176 Arabica coffees showed that geographical origin has a stronger impact on metabolite profiles than processing methods, with factors like altitude and variety also playing important roles, though to a lesser extent [108]. This suggests that the same processing technique applied across different regions can yield different outcomes due to differences in climate, soil, and the inherent composition of coffee beans. For example, while washed processing typically lowers sugar content through fermentation and leaching, the degree of sugar loss and its sensory effects may vary depending on the native sugar levels, which are influenced by altitude and genetic background [108,109].

Additionally, differences in methods across studies make direct comparisons challenging. Targeted analyses generally concentrate on known precursors such as chlorogenic acids and caffeine. In contrast, untargeted metabolomics uncovers wider changes in lipid pathways, organic acids, and nitrogen-containing compounds [108,110]. The presence of malic acid derivatives or certain phenolamides in some studies but not in others may be due to analytical sensitivity, sample preparation, or actual differences related to bean origin and processing details [108,111].

Importantly, abiotic stresses caused by processing, such as drought during drying or hypoxia during fermentation, trigger specific metabolic responses that alter metabolite profiles [109]. For instance, anaerobic conditions in honey processing encourage the production of certain amides and organic acids, whereas sun-drying tends to better maintain the original phenolic and amino acid compounds [107]. These stress-response mechanisms, influenced by local microbiota and processing conditions, partly account for why similar methods can yield different flavor chemistries.

In summary, primary processing significantly influences coffee flavor by changing the non-volatile metabolome. However, its effects depend on context and are intertwined with factors like origin, altitude, and variety. Future research should use integrated experimental designs that account for these variables, utilize consistent metabolomic platforms, and connect specific metabolite changes to sensory results with strong statistical models. Only through such systematic analysis can we advance from simple descriptions to predictive insights into how processing impacts coffee quality.

5.2. Advances in Fermentation Technologies to Improve Coffee Flavor

Although the main goal of fermentation in coffee processing is to remove mucilage from the beans [112], recent studies highlight its key role in influencing coffee flavor and quality. Fermentation helps break down unwanted compounds and encourages beneficial microbial metabolites to enter the beans. This process changes the aroma precursor profile in GCBs, ultimately impacting the sensory qualities of the final coffee [113]. Thus, fermentation is seen not just as a processing step but as an essential method for shaping flavor.

The impact of the fermentation method is clear in comparative studies [114]. For example, wet fermentation significantly improves flavor, aroma, and overall sensory scores compared to mechanical demucilaging, highlighting the microbial biochemical contribution beyond physical removal [115]. Modern fermentation techniques increasingly use selected microbial inoculants comprising yeasts and lactic acid bacteria (LAB) to initiate the process. These inoculants enhance sensory profiles and safety, and may provide health benefits [116,117]. They work by producing enzymes such as cellulases, pectinases, amylases, proteases, and lipases, which break down complex bean substrates, releasing precursors for key volatile compounds that shape coffee aroma [116,117,118,119]. The involved microbial ecology is complex and varies, as metagenomic studies indicate that the structure of the microbiome and its metabolic output are heavily influenced by factors such as coffee variety, fermentation method (aerobic, anaerobic, submerged), altitude, and process duration [120]. This variability might lead to differences in outcomes reported across studies using similar inoculants under different conditions.

Besides using alive inoculants, applying enzyme preparations directly offers a focused method to boost process efficiency and flavor. For instance, pectinase specifically breaks down pectin in the mucilage, reducing fermentation time from the usual 36–72 h to as short as 24 h, thus decreasing the risk of off-flavor development linked to extended fermentation [121]. Likewise, carboxypeptidase has been employed to enhance certain aromatic notes and improve sensory qualities like aftertaste and mouthfeel [122]. The effectiveness of both microbial and enzymatic strategies depends on precise control of fermentation conditions. The use of automated bioreactors for real-time monitoring and adjusting temperature, pH, and dissolved oxygen levels has been vital. This creates a stable, consistent environment that optimizes microbial activity or enzyme function, resulting in more uniform and higher-quality products [123,124].

Recent innovations go beyond traditional fermentation tanks. Techniques like micro-sprouting where wet-processed GCBs are soaked followed by drying which induces biochemical changes in the bean, modifying its microstructure and composition. This pre-roasting process has been shown to lower caffeine and acrylamide levels while enhancing fruity aromas in the roasted coffee [125]. Additionally, the careful addition of flavor precursors, such as specific low molecular weight sugars during anaerobic germination, can intensify Maillard and caramelization reactions during roasting. This results in a richer aroma profile and higher sensory scores [126].

These advancements are transforming coffee processing from a traditional “treatment” phase to an era emphasizing “precision control” and “flavor design.” Currently, efforts are primarily concentrated on two areas, precise fermentation of coffee cherries with chosen inoculants and post-fermentation processes such as anaerobic micro-sprouting of GCBs (see Figure 4). Different microbial communities have been shown to generate unique aromatic profiles, paving the way for the development of tailored flavors [118]. This expanding potential increases the demand for selecting, optimizing, and scaling specific fermentation starters.

However, significant knowledge gaps remain, creating a “black box” in our overall understanding. While research actively explores functional starters such as yeasts, LAB, and acetic acid bacteria, and works to optimize fermentation conditions like temperature, pH, and oxygen levels, few studies clarify exactly how these factors direct microbial succession and metabolic pathways. The specific mechanisms by which microbes and enzymes convert precursors (sugars, amino acids, organic acids) into volatile aromas remain poorly understood. Additionally, research has focused mainly on volatile aroma compounds, often overlooking the essential role of non-volatile components (such as sugars, acids, chlorogenic acids, and caffeine) in shaping key sensory qualities like body, acidity, bitterness, and aftertaste.

Future studies should focus on mechanistic research that combines multi-omics methods (like metagenomics and metabolomics) to explore the intricate connections between process variables, microbial communities, and metabolite production. The aim is to turn coffee fermentation from an empirical process into a predictable and controllable system. Understanding these interactions at a microscopic level is crucial for tackling broader issues related to standardization, sustainability, and economic efficiency at farms. This knowledge will support the reliable production of coffees with customized and higher quality.

6. Green Coffee Bean Storage

6.1. Factors Affecting Coffee Bean Quality During Storage

Freshness plays a crucial role in determining the commercial value and safety of GCBs. During storage, GCBs undergo complex physicochemical changes, mainly due to lipid oxidation, a process that accelerates at higher temperatures, in the presence of oxygen, and under light exposure [127,128]. Research consistently shows that storing at higher temperatures (such as 40–60 °C) significantly increases acid value, peroxide value, and free fatty acids, while reducing unsaturated fatty acids. These changes are directly linked to faster deterioration in quality and a shorter shelf life [127,129,130]. Importantly, Arrhenius-based models predict a much shorter shelf life at elevated temperatures, underscoring the need to control storage temperature to preserve quality [127].

Besides temperature and humidity, packaging also influences quality changes. Higher water activity promotes microbial growth and increases mycotoxin risk [131,132], while packaging permeability affects how well volatiles are retained and the oxidative stability. For example, GrainPro bags more effectively preserve water activity and volatile profiles compared to jute bags under the same conditions, although temperature generally has a stronger impact than packaging [133]. Volatile compounds such as hexanal and methional serve as indicators of storage-related oxidation, with their accumulation associated with rancid off-flavors [127,133,134].

However, the literature shows that results vary depending on factors such as coffee species (Arabica vs. Robusta), processing method (natural vs. washed), and initial quality. For example, washed beans generally exhibit a slower increase in free fatty acids than natural ones under similar storage conditions, highlighting how pre-storage treatments interact with storage conditions [133]. These nuances indicate that a critical synthesis is necessary, focusing on integrating factors like genetic material, post-harvest handling, and experimental conditions, rather than simply listing them in the design. Future work should systematically decouple these variables to refine storage protocols and predictive models that preserve coffee flavor and ensure safety.

In addition to diminishing the sensory quality of coffee beans, mold contamination poses a more serious threat by potentially producing mycotoxins that endanger human health. Several types of mycotoxins have been identified in coffee, including ochratoxin, aflatoxin B1 (AFB1), fumonisin B2, sterigmatocystin, beauvericin, and enniatin A [135,136]. Among them, ochratoxin A (OTA) presents the highest contamination risk in GCBs. OTA exhibits strong teratogenic, carcinogenic, hepatotoxic, and nephrotoxic properties, and is difficult to completely degrade during the high-temperature roasting process [135]. Consequently, it has drawn considerable attention from food safety authorities, producers, and consumers.

OTA is a fungal secondary metabolite mainly produced by Aspergillus and Penicillium species. Contamination can occur at any stage from fruit development to postharvest processing, through soil, equipment, or the surrounding environment. Critical stages such as fermentation, drying, and storage provide favorable conditions for mold growth, spore reproduction, and OTA synthesis, particularly under temperatures of 15–30 °C and water activity (aw) levels of 0.95–0.99 [137]. To minimize OTA formation during transportation and storage, the moisture content of coffee beans should not exceed 12.5%, with relative humidity maintained between 60% and 80% and aw ≤ 0.7 [138]. However, excessive drying, for instance, when the moisture content falls below 10% or aw drops to around 0.4, although inhibiting most microbial activity, adversely affects the basic metabolism in beans [139]. This accelerates the oxidative deterioration of key flavor precursors such as lipids and proteins, resulting in stale and flat-tasting coffee beans.

6.2. Innovative Strategies for Preserving Coffee Quality During Storage

Packaging is indispensable for the storage and transportation of commercial GCBs, representing the most direct and effective means of protection. Different packaging materials exert distinct influences on quality, stability, and storage duration [124]. Jute sacks are the most prevalent for storing GCBs [140]. However, jute sacks struggle to preserve the original chemical composition, sensory attributes, and color quality of coffee beans, and therefore are not suitable for long-term storage of specialty coffee [128,141]. Similarly, paper-based packaging provides unsatisfactory storage performance, preserving GCBs for only about six months [142]. In contrast, hermetic packaging is increasingly favored by specialty coffee traders [142]. Common options include vacuum-sealed bags, GrainPro^® bags, and pouches made of high-density polyethylene (HDPE) or low-density polyethylene (LDPE). A promising sustainable approach involves combining high-barrier plastic films like LDPE with natural jute bags, which enhances the latter’s resistance to moisture, insects, and microbial contamination [143]. Another advanced strategy involves the use of edible coatings. Interestingly, these polymer coatings can be applied either as packaging components or directly onto the bean surface. They melt and detach during roasting, thus exerting no adverse impact on the sensory attributes of the final product, which is of considerable importance for quality preservation [144].

The protective function of packaging can also be significantly enhanced by modifying the internal atmosphere. When hermetic packaging is combined with modified atmosphere technology, oxygen exposure to GCBs is substantially reduced, thereby suppressing oxidative reactions and respiration and ultimately extending shelf life. For example, injecting 60% carbon dioxide into sealed packaging has been shown to maintain the color and sensory attributes of GCBs for up to 12 months [145]. However, possibly because of higher costs and established trade practices, the use of modified-atmosphere technology in recent years has been mostly limited to roasted and instant coffee products [146]. Research on its use for raw GCBs remains limited, and data on optimal gas composition, packaging materials, and conditions during logistics and transportation are still lacking.

In addition, GCBs, as an agricultural product, are known to be highly vulnerable to fungal contamination during processing and storage. This contamination can diminish sensory qualities and also result in mycotoxin buildup, which could pose health risks to consumers [131]. However, sterilization technologies appear to be rarely applied on a large scale during GCB processing. As summarized in

Table 1. Applications of technologies for maintaining the quality of stored coffee beans.

Types of Technique	New Techniques/ Materials	Technical Features	Type of Coffee Beans	Beneficial Effects	References
Packaging	High density polyethylene (HDPE) bag	Excellent barrier properties to gas and water vapor	GCBs (Coffea arabica L. cv. Catimor)	Preserved the moisture content (7.83–10.28%), colour and chlorogenic acid in beans up to 1 year of storage.	[140]
Packaging	Hermetic/GrainPro® bag	Low air permeability	GCBs (Caffea arabica L.)	Delayed oxidation and maintained bean quality under accelerated storage, aw of beans ranged from 0.53 to 0.47.	[127]
Packaging	Plastic packages combined artificial atmosphere	High-barrier property	Special GCBs (Coffea arabica L.)	Low values of fat acidity and free fatty acids. Maintained water content between 9.87% and 10.30%, and high cup scores (80–84 points, special grade) after 12 storage months	[128]
Coating	Modified cassava starch coatings	High resistance to moisture, uniform adhesion and odorless	GCBs (Coffea arabica L.)	Retained the original physical characteristics (color and moisture) of the bean and beverage sensory.	[156]
Coating	Active coatings of chitosan with α-tocopherol	Good adherence and hydrophobic character	Special GCBs (Coffea arabica)	Protected coated beans from compression of atmospheric water vapor during storage.	[144]
Sterilizing	ClO2 gas treatment	Efficient inactivationbut present safety risks residual chlorine	GCBs (Coffea arabica L.)	Completely inactivated Aspergillus flavus and prevented its growth on beans within 12 days of storage.	[157]
Sterilizing	Menthol and eugenol in vapor treatment	Great antifungal activity	GCBs (Coffea arabica L.)	Protected beans from Aspergillus parasiticus contamination (above protection level of 62.50% and 73.21%)) during 12-month storage.	[131]
Sterilizing	Formic acid vapor treatment	Effective disinfectant	GCBs (Coffea arabica L.)	Prevented growth of mold during storage, with the spores count being below the detection limit (1.7 log cfu/5 beans). Minorly impacted the color and pH of GCBs.	[158]
Sterilizing	Bacillus licheniformis M2-7	Effective disinfectant	Coffee beans (Coffea arabica L.)	Effectively inhibited fungal growth rates from 67.8% to 95.5% and reduced OTA concentration from 24.35 to 5.52 µg/kg.	[159]
Sterilizing	Yeasts (Rhodosporidiobolus ruineniae and Meyerozyma caribbica)	Potential biocontrol agents	Robusta coffee (Coffea canephora) cherries	Reduced Aspergillus carbonarius growth and OTA production by 85% and 90%.	[160]

, several physical, chemical, and biological sterilization methods have been explored to protect GCBs, yet their effectiveness and safety require further investigation and validation. It is noteworthy that microbial contamination remains a significant potential threat to both the quality and safety of coffee beans. Therefore, the development of safe and efficient food preservatives in the future will be essential to safeguard the commercial value of coffee beans and ensure the safety of the resulting beverage. In terms of OTA prevention and control, the implementation of Good Manufacturing Practices (GMP) and Hazard Analysis and Critical Control Point (HACCP) systems can help standardize coffee production processes. By identifying critical control points (CCPs) such as drying, storage, and transportation according to local environmental conditions and market requirements, these systems can effectively minimize the risk of mycotoxin contamination throughout the production chain [147]. Although the United States Food and Drug Administration (FDA), Codex Alimentarius, and the European Union (EU) have not established OTA limits for GCBs, several countries, including Italy, Finland, and Greece, have set maximum allowable OTA levels of 8, 10, and 20 μg/kg, respectively [135,148]. The European Commission has also specified OTA thresholds of 3 μg/kg for roasted coffee and 5 μg/kg for instant coffee [149]. Differences in national mycotoxin regulations, combined with limitations in detection technology, may hinder the efficiency of the coffee trade and export. In addition to conventional chromatographic and mass spectrometric techniques used in laboratory analysis [150,151], field-deployable detection methods such as immunochromatographic assays (ICA) and biosensors have gained increasing attention due to their convenience, high sensitivity, rapid detection, and low cost [152,153]. Chen et al. [154] developed an ICA method employing fluorescent nanoprobes as signal amplification probes for OTA detection in maize, achieving a limit of detection (LOD) of 0.042 ng/mL, substantially lower than previous reports (0.07–1.86 ng/mL) with a detection time of only 15 min and excellent reproducibility and accuracy. A 2025 study further demonstrated a dual-analyte immunostrip capable of simultaneously detecting OTA (LOD 5 ng/mL) and AFB1 (LOD 0.5 ng/mL) in cereal samples, showing strong consistency with HPLC results [150]. Argoubi et al. [155] developed electrochemical aptasensors for OTA with an exceptionally low LOD of 0.011 ng/mL and a recovery rate of 97% in roasted coffee samples, without requiring pretreatment or concentration steps. Although these emerging mycotoxin detection technologies are continuously improving, their application to GCBs remains limited. Expanding their use in coffee safety monitoring presents significant opportunities for future research and industrial implementation.

Although notable progress has been made in extending the shelf life of coffee beans, no commercial packaging technology currently available can fully preserve the quality of GCBs. Even under appropriate storage conditions, prolonged storage inevitably leads to slight deterioration in attributes such as appearance, structure, and flavor. Once this deterioration reaches an unacceptable level, the beans effectively lose their commercial value. Therefore, preventing quality degradation remains a critical challenge. In addition to optimizing storage conditions and packaging technologies, the initial sensory attribute of coffee beans plays a decisive role in determining quality stability during long-term storage [161]. It is essential to closely monitor key quality indicators during the storage of GCBs. Important factors to keep an eye on include sensory attributes, oxidation levels, water activity, microbial contamination, and OTA content. These parameters are closely linked to the overall quality of the stored beans. In particular, several spectroscopic techniques, such as Raman spectroscopy and 1H NMR spectroscopy [162,163], have been applied to monitor chemical changes in coffee beans during storage. These approaches provide new perspectives for quality control by enabling the early prediction of deterioration through the detection of characteristic compounds associated with spoilage, thereby strengthening the management of coffee quality throughout the storage period. So et al. [164] conducted an integrative statistical analysis combining mass spectrometry data with sensory evaluations and identified aroma compound levels as reliable quality control indicators for Ethiopian Yirgacheffe coffee during processing and storage. Compounds such as N-furfuryl pyrrole, a positive flavor contributor, and 2,4-bis(1,1-dimethylethyl)-phenol, a key negative aroma component, were proposed as markers whose concentration dynamics can guide the optimization of storage parameters to enhance flavor quality. However, focusing solely on chemical composition provides an incomplete perspective. Future research should aim to elucidate the formation and degradation mechanisms of these critical compounds and establish correlation models linking key chemical indicators with sensory attributes. Such efforts will contribute to the development of a more objective and practical storage quality control system, ultimately improving consumer acceptance.

7. Conclusions

High-quality coffee results from the synergistic interaction of genetic, ecological, agronomic, processing, and postharvest storage factors, including nutrient and shade management. Genetics establishes the fundamental potential for quality. In Coffea arabica, the allotetraploid genome influences key metabolites through homoeologous exchanges, structural variants, and historical introgression. Environmental conditions, including temperature, altitude, and water availability, modulate gene expression and metabolic pathways, while agronomic practices such as optimized shade and precision nutrient management help steer these pathways toward favorable outcomes. Postharvest processing, particularly controlled fermentation and anaerobic treatments, actively reshapes metabolite profiles and thereby enables targeted enhancement of sensory complexity. Storage conditions, supported by hermetic and active packaging, are critical for preserving these gains by slowing oxidative deterioration and microbial spoilage. Translating these mechanisms into practice requires an integrated strategy. This includes genetic improvement through haplotype-resolved genomes and marker-assisted selection, site-specific agronomic management, the adoption of starter cultures and anaerobic germination during processing, and the use of hermetic packaging coupled with rapid mycotoxin detection. Among these approaches, nutrient optimization, hermetic storage, and starter-assisted fermentation are the most readily implementable, whereas long-term genetic improvement and broader systemic solutions require sustained institutional support. A phased approach that focuses on immediate postharvest and storage improvements, while also investing in long-term genetic and systemic strategies, provides a practical route to achieve sustainable production of high-quality coffee.