The woody legume, mesquite (Prosopis glandulosa) has expanded from its historical habitats (playas and arroyos) to recently occupied grassland and dune habitats during the desertification of perennial grasslands in the Chihuahuan Desert. We studied historical and recently occupied sites, having hypothesized that the trophic structure and population density of soil microarthropods and nematodes associated with the surface root system of mesquite would differ in sites representing historical and recent habitats, and that the N mineralization potential would be lower in the recent habitats. Our results showed that net N mineralization potential did not differ significantly among the sites, even though soil nutrient concentrations and texture varied widely. Concentrations of organic C, N, and P were lowest in the recent dune habitat and highest at the playa. Very low concentrations of P in the dune and grassland soils implicated P as a limiting factor in these systems. The bacterial-feeding and omnivore-predator functional groups made up the largest fraction of the nematode community at most of the sites. The high density of plant-feeding nematodes at the playa indicated that herbivory is potentially most important at this site. Total microarthropod densities did not vary significantly among habitats, with Collembola densities highest in the mesquite dunes. Grazers were the dominant microarthropod functional group. While both C and N pool sizes were higher in the historical habitats, a higher substrate lability in the recent habitats appeared to support biota populations and N mineralization rates equivalent to those in the playa and arroyo. Differences in soil properties and biota among historical and recent mesquite habitats may be important for understanding the changes that have occurred in Chihuahuan Desert ecosystems during desertification.