<p>Understanding how microbial communities assemble is central to predicting ecosystem function. Although predators strongly influence bacterial communities through predation, the role of microbial predators in modulating global microbial divergence and convergence patterns remains largely neglected. Here, we integrated global-scale amplicon sequencing data, controlled field experiments, and reconstructions of natural and synthetic communities to examine predator-mediated community assembly mechanisms. We show that bacterivorous protists exert dual, scale-dependent effects on microbial communities: promoting local convergence by suppressing dominant bacterial taxa, while generating global divergence through species-specific predation effects. We find that predator identity and prey susceptibility jointly determine convergence outcomes. Communities dominated by predator-resistant taxa exhibit reduced convergence under predation pressure, revealing a predictable trait-based filtering mechanism. This work establishes bacterivorous protists as key, context-dependent agents of biogeography and suggests new opportunities for microbiome engineering, where targeted use of protists may steer microbial communities toward functional configurations that enhance soil health and ecosystem resilience.</p>