Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on microbial communities in the subsoil is limited. Here, we investigate the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We show that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we find that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.