BackgroundThe ecological functions of biocrusts and microbial assembly processes under nitrogen deposition remain poorly understood, despite their critical roles in desert ecosystems facing increasing atmospheric nitrogen inputs.MethodsA three-year field experiment in China's Gurbantunggut Desert tested three nitrogen forms (nitrate-N, ammonium-N, urea-N) across gradient doses on cyanobacteria- and moss-biocrusts. We combined high-throughput sequencing, enzymatic activity assays, structural equation modeling (SEM), and null-model analysis to assess microbial diversity, soil multifunctionality (C/N cycling enzymes), and community assembly mechanisms.ResultsHigh-throughput sequencing results indicated that bacterial diversity and richness within the biocrusts were more pronounced than those of diazotrophs and fungi, with the community composition influenced by nitrogen form, dose, and time. Ammonium-N was found to significantly reduce the soil multifunctionality and C/N cycling index in both types of biocrusts, while urea-N had the opposite effect. SEM identified pH, microbial biomass and exopolysaccharides as key mediators of nitrogen effects on biocrust stability. Null-model analysis further showed that stochastic processes dominated microbial assembly, but deterministic selection increased with ammonium-N exposure.ConclusionsUrea-N universally boosted productivity across biocrust types, while ammonium-N exhibited time-lagged ecotoxicity, culminating in 40% soil multifunctionality loss of biocrust after two years. Critically, nitrate-N shifted from stabilizing cyanobacteria-biocrusts at low doses to suppressing moss-biocrusts function at higher doses-underscoring ecosystem-specific nitrogen response frameworks. These varying trajectories of biocrusts highlight the need for tailored nitrogen management in dryland restoration.