Predatory protists, particularly ciliophoran *Colpoda* OTUs, negatively correlate with bacterial wilt disease incidence in tomato plants. Bioorganic fertilization enhances the abundance of predatory protists, which influence disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. The study demonstrates that predatory protists reduce bacterial wilt disease incidence in tomato plants through both direct and indirect reductions of pathogens, providing insights into the role of predatory protists in plant disease management and potential applications in sustainable agriculture.Predatory protists, particularly ciliophoran *Colpoda* OTUs, negatively correlate with bacterial wilt disease incidence in tomato plants. Bioorganic fertilization enhances the abundance of predatory protists, which influence disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. The study demonstrates that predatory protists reduce bacterial wilt disease incidence in tomato plants through both direct and indirect reductions of pathogens, providing insights into the role of predatory protists in plant disease management and potential applications in sustainable agriculture.