1. Soil disturbance by animals affects the availability of water, nutrients, sediment and seeds, which are critical for the maintenance of functional ecosystems. We examined long-lived faunal structures across six vegetation communities in the northern Chihuahuan desert of New Mexico, USA, testing the proposition that disturbances in undesertified grassland differ in magnitude and effect from those in desertified grassland. 2. Vertebrate and invertebrate disturbances totalled 18.9 structures ha⁻¹ across 18 sites. The most common were pits and mounds of American badgers (Taxidea taxus, 32%), nests of the ant Aphaenogaster cockerelli (18.8%) and mounds of kangaroo rats (Dipodomys spectabilis, 31%). 3. Desertification was associated with a doubling of the density of structures, but no effects on cover or volume. The greatest density was in desertified mesquite and creosote bush shrublands, and the lowest density in undesertified grass swales. Badger and wood rat (Neotoma sp.) mounds were significant indicators of desertified communities. 4. Desertification did not affect the density of kangaroo rat mounds (6.7 ha⁻¹ in black grama grasslands and creosote bush shrublands). However, mounds in creosote bush shrubland were smaller and had more and larger shrubs than adjacent inter-mound hummocks. Desertification was associated with increases in the density of Aphaenogaster cockerelli and Trachymyrmex smithii nests, and declines in Pogonomyrmex rugosus nests. Substantial increases in soil nitrate and electrical conductivity on Myrmecocystus nests were associated with desertification. 5. Synthesis. Desertification shaped this desert environment in two main ways. First, while kangaroo rat mound density changed little with desertification, mounds in shrubland continued to enhance shrub persistence long after abandonment, reinforcing desertification processes. Second, marked changes in the density of nests of the key ant species altered the spatial distribution of soil nitrate and electrical conductivity, likely affecting soil fertility and the distribution of desert plants. Our results highlight the importance of animal activity in shaping desert plant communities, and in maintaining or reinforcing desertification processes.