Microbial activities are of particular interest in Arctic and Antarctic soils due to the uncertainty surrounding the fate of the vast permafrost reserves and potential to lose unique and vulnerable communities. We identified the richness, evenness and taxonomic composition of fungi and bacteria in 223 Arctic and Antarctic soil samples. We generated multiple alternative structural equation models to identify causal external controls on these communities. Analysing bacterial and fungal data from both poles allowed us to test the suitability of emerging hypotheses concerning drivers of soil microbial communities developed primarily for bacteria and primarily in temperate and tropical systems. Soil fertility was the most important control on richness and evenness, whereas pH was the key controller of structure and phylogenetic divergence. Phosphorus availability was the next most important influence on all facets of the microbial ecosystems. Our results suggest that textural control is indirect and largely mediated through the effect of soil particle size on pH. The role of mineralogy is less clear, with large but inconsistent direct effects and consistent indirect effects through the mediation of phosphorus and pH in the soil ecosystem. The key difference between fungi and bacteria is that fertility plays a much larger role for fungal communities and acidity for bacterial communities.