SummaryRoots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe–plant links are not completely understood.Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and β‐diversity) in a dry Mediterranean scrubland.We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial β‐diversity was related to root β‐diversity, while fungal β‐diversity was related to aboveground plant β‐diversity, suggesting that plants differently influence both microbial groups.Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities.