Soil protists significantly influence ecosystem multifunctionality (EMF) through their roles in microbial predation, parasitism, and organic matter decomposition. However, the multifaceted contributions of protist diversity, along with its interactions with other microbial groups and plant diversity, to EMF—especially under climate-induced stresses such as drought—remain poorly understood. To address this knowledge gap, we conducted a factorial microcosm experiment, manipulating microbial diversity (protists, bacteria and fungi), plant species richness, and drought stress. In total, 203 microcosms were established, generating 812 soil samples and 2436 amplicon sequencing libraries. Using structural equation modelling (SEM) and multiple regression analyses, we found that protist diversity was positively correlated with EMF, carbon sequestration, soil organic matter (SOM) decomposition, and nutrient cycling. Furthermore, protist communities exhibited distinct, phylum-specific relationships with these ecosystem functions. Under drought conditions, microbial interaction networks experienced significant restructuring, with protists emerging as keystone taxa—enhancing protist connectivity and highlighting their central role in ecosystem resilience, especially in relation to leaf carbon dynamics. Our findings provide novel empirical evidence that protists act as multitrophic integrators in soil ecosystems and highlight their role in buffering ecosystems against global environmental change.