Plant-beneficial microbes improve while pathogens reduce plant performance. When introduced in soils, such microbes can induce entire microbiome changes. However, the impact of those microbial introductions on protists – key predators within the soil microbiome – remain unknown. Here, we tracked how soil protists respond to bacterial (Bacillus and Ralstonia) and fungal (Trichoderma and Fusarium) introductions, with both microbial groups represented by one beneficial and one pathogenic taxon. We found that plant-beneficial Bacillus bacteria change the protist community structure. This community-shift was likely induced by an increased fungi/bacteria ratio, supported by a negative correlation of the fungi/bacteria ratio with the relative abundance of phagotrophic protists across all treatments. Our results indicate that microbial introductions can impact protist communities, thereby altering microbiome-derived multi-functionality.