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The comprehensive analysis of microbial communities reveals the unique microbial identity of different olive varieties, paving the way for new strategies in their development and commercial exploitation. In this context, the present study aimed to explore the microbial diversity and functional characteristics of Tsounati variety olives from the Monemvasia region of Peloponnese, Greece, that were naturally fermented for three months. The bacterial and fungal microbiota of both olives and brines were fingerprinted throughout the fermentation through classical microbiological analysis combined with molecular techniques. Among the 148 isolated bacteria, 85 were lactic acid bacteria (LAB), and 63 belonged to the Enterobacteriaceae family, while the 178 fungal isolates comprised 136 yeasts and 42 non-yeast or yeast-like fungi. Metataxonomic analysis confirmed the dominance of the bacterial genera Lactiplantibacillus, Leuconostoc, along with the Enterobacteriaceae family, and it revealed the presence of Coleofasciculaceae cyanobacteria mostly in olives. The dominant fungal genera were yeasts, namely Saccharomyces, Nakazawaea, and Cyberlindnera. Using the Folin–Ciocalteu assay, the average total polyphenol content of Tsounati fermented olive samples was 761.80 ± 128.87 mg gallic acid equivalents kg⁻¹ after 90 days of fermentation. The concentrations of the triterpenic, maslinic, and oleanolic acids, as determined by HPLC, remained stable throughout fermentation, with average values of 4764 and 1807 mg kg⁻¹, respectively. Finally, sensory analysis revealed the rich aromatic character of Tsounati variety, highlighting its potential to be used for Greek-style table olive production. Full article