Biological soil amendments are known to benefit crop production, yet their interaction with different soils and management practices remains poorly understood. Accordingly, this study investigated and compared the effects of Compost, Bokashi, and Trichoderma on soil and tomato fruit quality across different field conditions. The research used a multi-site field experiment involving six tomato greenhouses in a Mediterranean area of central Chile. Within each greenhouse, tomato plants were cultivated in soils amended with Compost (C), Bokashi (B), and Trichoderma (T), alongside an unamended control soil (O). Then, the impact of these treatments was compared among them regarding soil chemistry, the abundance of plant growth-promoting rhizobacteria and tomato fruit quality traits. Bokashi outstood significantly increasing soil organic matter, nitrogen, phosphorus, and potassium levels compared to the Control. All amendments increased the abundance of plant growth-promoting rhizobacteria and anthraquinone in tomatoes. On the other hand, tomatoes in Trichoderma-treated plots showed higher phenolic content but smaller fruit sizes. Other tomato quality traits were better explained by producer effect, that is, local management and/or conditions, than by the effect of the amendments (e.g., fruit weight and lycopene concentration). We finally found that the abundance of Actinomycetes and a soil quality index could help predict the impact of the biological amendments. Altogether, our findings underscore the need to tailor soil amendments based on specific site conditions to maximize their benefits, especially within a more sustainable agriculture framework.