The distribution of soil nutrients in deserts is heterogeneous, with high concentrations of organic and inorganic nutrients occurring under shrubs and near animal dwellings. Attention has focused on shrubs in creating “fertile islands.” In this study, we compare the effects of the harvester ant Pogonomyrmex rugosus Emery (Hymenoptera: Formicidae) and shrubs on soil composition in the Mojave Desert. Soil organic matter, total N, mineral N, and available P were significantly more concentrated in the nests of P. rugosus than under the dominant vegetation and in sparsely vegetated interspaces between shrubs and ant nests. Ant nests also contained high concentrations of total C, organic C, and soluble organic C and N relative to other microhabitat types. On an areal basis, ant nests stored 3% of mineral N and 0.7–1.6% of organic matter, total N, and available P on the landscape while covering 0.5% of the surface. At field moisture, microbial biomass C and N were significantly more concentrated in ant nests at one of two study sites. When moistened, ant nest soils had a higher capacity for microbial growth than soils from other microhabitats. As a result of ant activities, ant nests accumulated surface materials at an average rate 3.5 mm/yr faster than the surrounding soil. We conclude that P. rugosus nests impact arid ecosystems by creating highly concentrated patches of soil nutrients and microflora on the landscape that could affect biogeochemical cycling rates and plant community dynamics.