Background and aims Nitrogen (N) deposition and climate change are a threat to the structure and function of drylands, where biocrust-dominated communities are prevalent. We aimed at evaluating the influence of N deposition, climate and edaphic properties of semiarid areas of Spain on soil microbial communities and N cycling. Methods We quantified soil bacteria, fungi, ammonium oxidizing bacteria and archaea, estimated the abundance of autotrophic organisms (soil pigment content) and measured a wide array of variables related to the N cycle. Results Local climatic conditions and soil fertility were main drivers of soil microbial communities and N cycling. In particular, cyanobacteria were favored in colder sites with lower soil fertility. Higher precipitation at high-fertility sites favored green algae. Soil N availability was negatively related to MAT. Increased N deposi-tion (4.3–7.3 kg N ha −1 yr. −1) reduced the abundance of soil bacteria and fungi, a response partially attributed to N-driven soil acidification, whereas it favored green-algae and increased available N in soil, contributing to a net ecosystem eutrophication. Conclusions Changes in soil microbial community structure and nutrient cycling in response to N deposi-tion and climate change will affect the overall functioning of semiarid Mediterranean ecosystems, which may have important implications in terms of long-term soil C sequestration.