The short-term responses of soil quality indicators are important for assessing the effects of new management practices and addressing threats to crop yields in greenhouses. The aim of this study was to assess, during three consecutive cropping seasons, the effect of a sustainable management package (CRTMP)—which includes the on-site reuse of greenhouse crop residues and tillage—in comparison with conventional management, based on fertigation only (CMP), on certain biochemical soil quality indicators and crop yields. CRTMP significantly increased (p
< 0.05) the values of total organic carbon (TOC), particulate organic carbon (POC), light fraction (LF), water soluble organic carbon (WSOC), and dehydrogenase (DH) and β-glucosidase (GL) activities at a depth of 0–15 cm, as well as the mean concentration of nitrates in the soil solution. In addition, a significant Pearson’s correlation (p
< 0.01) found between the indicators suggested a balanced improvement of soil biological activity and nutritional soil state. Nonetheless, the significant (p
< 0.05) increases in the mean concentration of chlorides in the soil solution and electrical conductivity (p
< 0.05) increased the risk of salinization, which may have affected the concentration of nitrates in the petiole sap and total production in CRTMP, which were significantly lower than in CMP. Nevertheless, the proportion of premium product was significantly higher in CRTMP, while the proportion of non-commercial production decreased.
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