Organic farming can enhance biodiversity and soil health and is a sustainable alternative to conventional farming. Yet, soil protists especially protistan predators, have received inadequate attention, and their contributions to the sustainability of organic farming remained underexplored. In this study, we examined soil microbial communities from 379 samples, including both organic and chemically fertilized soils from China. Our findings revealed higher bacterial diversity and increases in plant-beneficial bacteria in organically farmed soils. Notably, organic farming systems facilitated dynamic predator-prey interactions, which may be disrupted by the application of chemical fertilizers. Additionally, organic farming enriched protistan predators, enhancing the relative abundance of functional PGPR, thus improving soil health. We further conducted a case study highlighting the critical role of organic matter in sustaining protistan predator populations and their interactions with bacteria. We propose the crucial contributions of organic inputs for supporting protistan predators and the interplay of predator-prey, ultimately enhancing soil functions and promoting agricultural sustainability.