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Interactions between plants and soil microbes influence plant nutrient transformations, including nitrogen (N) fixation, nutrient mineralization, and resource exchanges through fungal networks. Physical disturbances to soils can disrupt soil microbes and associated processes that support plant and microbial productivity. In low resource drylands, biological soil crusts (“biocrusts”) occupy surface soils and house key autotrophic and diazotrophic bacteria, non‐vascular plants, or lichens. Interactions among biocrusts, plants, and fungal networks between them are hypothesized to drive carbon and nutrient dynamics; however, comparisons across ecosystems are needed to generalize how soil disturbances alter microbial communities and their contributions to N pools and transformations. To evaluate linkages among plants, fungi, and biocrusts, we disturbed all unvegetated surfaces with human foot trampling twice yearly from 2013–2019 in dry conditions in cyanobacteria‐dominated biocrusts in the Chihuahuan Desert grassland and shrubland ecosystems. After 5 years, disturbance decreased the abundances of cyanobacteria (especially Microcoleus steenstrupii clade) and N‐fixers (Scytonema sp., and Schizothrix sp.) by >77% and chlorophyll a by up to 55% but, conversely, increased soil fungal abundance by 50% compared with controls. Responses of root‐associated fungi differed between the two dominant plant species and ecosystem types, with a maximum of 80% more aseptate hyphae in disturbed than in control plots. Although disturbance did not affect 15N tracer transfer from biocrusts to the dominant grass, Bouteloua eriopoda, disturbance increased available soil N by 65% in the shrubland, and decreased leaf N of B. eriopoda by up to 16%, suggesting that, although rapid N transfer during peak production was not affected by disturbance, over the long‐term plant nutrient content was disrupted. Altogether, the shrubland may be more resilient to detrimental changes due to disturbance than grassland, and these results demonstrated that disturbances to soil microbial communities have the potential to cause substantial changes in N pools by reducing and reordering biocrust taxa.