Crop diversification practices are expected to influence soil carbon (C) dynamics by altering microbial communities, yet their effects across environmental contexts and on carbon use efficiency (CUE) remain unclear. We tested whether diversified cropping systems modify microbial alpha diversity and community composition, and whether they alter diversity-function relationships. To do so, we analysed fungal and bacterial communities and CUE in soils from six countries along a pan-European gradient. Microbial composition was strongly structured by environmental context, particularly for fungi. After accounting for this context, crop diversification explained a small but significant fraction of variation in both bacterial and fungal communities. However, responses differed between microbial groups, with bacterial communities showing consistent but minor shifts, whereas fungal responses were highly context dependent. Crop diversification did not affect bacterial alpha diversity, measured as richness and Shannon diversity, but had a marginal, context-dependent effect on fungal richness. Although crop diversification did not directly affect CUE, it modified the relationship between fungal Shannon diversity and CUE, with a weak negative association under control conditions which disappeared under crop diversification. This interaction was driven by microbial respiration rather than microbial growth, indicating shifts in C loss pathways. Overall, our findings show that crop diversification subtly reshapes microbial communities within strong environmental constraints and can alter diversity-function relationships, highlighting the context dependency of soil C stabilization.