Human activities have doubled, or even tripled, the amount of nitrogen (N) fixed globally, which alters the functioning and reduces the biodiversity of terrestrial ecosystems. In this study, we used a 10‐year N addition experiment in a semi‐arid Mediterranean shrubland in central Spain to evaluate the effects of increased N deposition on biocrust cover, soil microbial enzymatic activity and their spatial patterns. We collected highly replicated, spatially explicit data to carry out Moran's I correlograms at the plot level and used linear mixed models to evaluate the effects of N addition on cover, microbial activity and Moran's I values for each distance class of correlograms. High N deposition (50 kg N ha−1 year−1) reduced the cover of the foliose lichen Cladonia foliacea, an important component of biocrusts, and generated significant alterations and losses of the spatial pattern of biocrusts and soil microbial enzymatic activity. Furthermore, we found indication that N addition altered the relationship between biocrust cover and microbial enzymatic activity, suggesting that the presence of well‐developed biocrust communities modulates the effects of high N deposition on soil microbial activity. Synthesis. Overall, our study suggests that an increase in N deposition may have important consequences for the structure and functioning of Mediterranean ecosystems and that some of these consequences may be due to alterations in the way in which different soil communities (e.g. moss‐lichen biocrusts and soil microorganisms) interact with one another. A free Plain Language Summary can be found within the Supporting Information of this article.