Many ecosystem services are sustained by the combined action of microscopic and macroscopic organisms, and shaped by interactions between the two. However, studies tend to focus on only one of these two components. We combined the two by investigating the impact of macrofauna on microbial community composition and functioning in the context of a major ecosystem process: the decomposition of dung. We compared bacterial communities of pasture soil and experimental dung pats inhabited by one (Aphodius), two (Aphodius and Geotrupes), or no dung beetle genera. Overall, we found distinct microbial communities in soil and dung samples, and that the communities converged over the course of the experiment. Characterising the soil microbial communities underlying the dung pats revealed a significant interactive effect between the microflora and macrofauna, where the diversity and composition of microbial communities was significantly affected by the presence or absence of dung beetles. The specific identity of the beetles had no detectable impact, but the microbial evenness was lower in the presence of both Aphodius and Geotrupes than in the presence of Aphodius alone. Differences in microbial community composition were associated with differences in substrate usage as measured by Ecoplates. Moreover, microbial communities with similar compositions showed more similar substrate usage. Our study suggests that the presence of macrofauna (dung beetles) will modify the microflora (bacteria) of both dung pats and pasture soil, including community diversity and functioning. In particular, the presence of dung beetles promotes the transfer of bacteria across the soil–dung interface, resulting in increased similarity in community structure and functioning. The results demonstrate that to understand how microbes contribute to the ecosystem process of dung decomposition, there is a need to understand their interactions with larger co-occurring fauna.