Soil bacteria and fungi are key drivers of carbon released from soils to the atmosphere through decomposition of plant-derived organic carbon sources. This process has important consequences for the global climate. While global change factors, such as increased temperature, are known to affect bacterial- and fungal-mediated decomposition rates, the role of trophic interactions in affecting decomposition remains largely unknown. We designed synthetic microbial communities consisting of eight bacterial and eight fungal species and tested the influence of predation by a model protist, Physarum polycephalum, on litter breakdown at 17 and 21 °C. Protists increased CO2 release and litter mass loss by ~35% at 17 °C lower temperatures, while they only had minor effects on microbial-driven CO2 release and mass loss at 21 °C. We found species-specific differences in predator–prey interactions, which may affect microbial community composition and functioning and thus underlie the impact of protists on litter breakdown. Our findings suggest that microbial predation by fast-growing protists is of under-appreciated functional importance, as it affects decomposition and, as such, may influence global carbon dynamics. Our results indicate that we need to better understand the role of trophic interactions within the microbiome in controlling decomposition processes and carbon cycling.