Soil microbial communities are vital for multiple ecosystem processes and services. In particular, soil microbial food webs are key determinants of soil biodiversity, functioning and stability. Unclear, however, is how structural features of food webs, such as species richness and turnover, biomass and energy transfer across trophic levels, influence the provisioning and stability of ecosystem functioning. Here, we explore the relationships between different facets of microbial food web structure (e.g. species richness, connectance, biomass and energy fluxes across trophic levels) and ecosystem functions (i.e. decomposition and microbial enzyme activity) across different habitats and depths in a peatland. We show that no aspect of taxonomic richness directly explained variation in ecosystem functions. Instead, we find that trophic interactions between basal species and primary consumers, and especially increasing connectance, biomass and energy flux transiting from decomposers and phototrophs to algivores, bacterivores and fungivores, enhance ecosystem functions in the peatland. These findings demonstrate that focusing on taxonomic diversity without explicit inclusion of food web structure and energy flows therein gives an incomplete and uninformative comprehension of relationships between biodiversity and ecosystem functioning, at least in peatlands. Our findings further suggest that the inclusion of soil microbial food webs in large-scale biogeochemical models is of fundamental importance to provide the necessary guidance for managing and mitigating the effects of environmental change.