Traditionally, restoration projects have focused on replacing non-native plants with native species, and assumed that restored ecosystem function would follow. However, increasing evidence indicates that function does not always follow form, particularly in highly altered environments such as urban areas. Humans manipulate the urban environment directly through irrigation, fertilization, and pruning, as well as indirectly through urban heat islands and the deposition of air pollution. We explored the relationship between native plants and belowground nutrient cycling across a gradient of human manipulation in Phoenix, Arizona. Three landscape types were considered: undisturbed Sonoran desert outside the city, desert preserves within the urban airshed, and “restored” desert landscapes planted with native species within xeriscaped residential yards. We measured soil nutrient pools and dynamics with a spatially explicit sampling design surrounding two native Sonoran desert plants common in residential landscaping: Brittlebush (Encelia farinosa, a fast growing shrub) and Palo verde (Parkinonia spp., a nitrogen-fixing tree). Inorganic soil nitrogen (N) and organic matter pools beneath Palo verde trees were statistically similar among sites, regardless of position within the urban landscape. In contrast, resource pools beneath brittlebushes were elevated inside the city. In fact, scaling up according to patch cover, exposure to the urban climate doubled inorganic soil N from 16.6 μg N/gram dry soil in outlying desert to 33.5 μg N/gram dry soil in urban desert. Soil organic matter and net potential N cycling were also elevated in urban compared to outlying desert sites. In contrast, human management in xeriscaped yards altered few soil properties beyond the effects of the urban atmosphere.