Industrial farming without considering soil biological features could lead to soil degradation. We aimed to evaluate the biochemical properties (BPs) and biological fertility (BF) of different soils under processing tomato cultivation; estimate the BF through the calculation of a simplified BF index (BFIs); determine if the crop was affected by BP and BF. Three farms were individuated in Modena (MO), Ferrara (MEZ) and Ravenna (RA) provinces, Italy. Soil analysis included total and labile organic C, microbial biomass-C (Cmic) and microbial respiration measurements. The metabolic (qCO₂), mineralization (qM) and microbial (qMIC) quotients, and BFIs were calculated. Furthermore, plant nutrient contents were determined. The low Cmic content and qMIC, and high qCO₂ found in MEZ soils indicate the occurrence of stressful conditions. The high qMIC and qM, and the low qCO₂ demonstrated an efficient organic carbon incorporation as Cmic in MO soils. In RA soils, the low total and labile organic C contents limited the Cmic and microbial respiration. Therefore, as confirmed by the BFIs, while MO showed the healthiest soils, RA soils had an inefficient ecophysiological energy state. However, no effects on plant nutrient contents were observed, likely because of masked by fertigation. Finally, BP monitoring is needed in order to avoid soil degradation and, in turn, crop production decline.