Biocrusts are key drivers of the structure and functioning of drylands and are very sensitive to disturbance, including atmospheric nitrogen (N) deposition. We studied the impacts of simulated N deposition on biocrust community composition and soil photosynthetic and photoprotective pigment content after five years of N application in a European semiarid Mediterranean shrubland. The experiment consisted in six experimental blocks with four plots, each receiving 0, 10, 20, or 50 kg NH4NO3-N ha−1 year−1 + 6–7 kg N ha−1 year−1 background. After 5 years of N application, total lichen cover decreased up to 50% compared to control conditions and these changes were only clearly evident when evaluated from a temporal perspective (i.e. as the percentage of change from the first survey in 2008 to the last survey in 2012). In contrast, moss cover did not change in response to N, suggesting that biocrust community alterations operate via species- and functional group-specific effects. Interestingly, between-year variations in biocrust cover tracked variations in autumnal precipitation, showing that these communities are more dynamic than previously thought. Biocrust species alterations in response to N were, however, often secondary when compared to the role of ecologically relevant drivers such as soil pH and shrub cover, which greatly determined the composition and inter-annual dynamics of the biocrust community. Similarly, cyanobacterial abundance and soil pigment concentration were greatly determined by biotic and abiotic interactions, soil pH for pigments, and organic matter content and shrub cover for cyanobacteria. Biocrusts, and particularly the lichen component, are highly sensitive to N deposition and their responses to pollutant N can be best understood when evaluated from a temporal and multivariate perspective, including impacts mediated by interactions with biotic and abiotic drivers.