Urbanization has dramatically altered habitats for local species worldwide. While some species are unable to meet the challenges that these alterations bring, others are able to persist as long as a threshold for suitable habitat is met. For reptiles, a key feature for persistence in urban areas can be access to suitable refuges from predation, high temperatures, and/or other environmental challenges. We tested for effects of local and landscape variables affecting urban occupancy in the Western Fence Lizard, Sceloporus occidentalis, in transects across an urban–rural gradient, with a specific focus on the presence of rock, tree, and shrub refuges. We found that fence lizards were much more likely to be present in areas with more rock cover, and in parks or low-density residential areas. Occupancy was also positively related to canopy cover in the general vicinity, though negatively related to number of trees along the transects. Our results highlight the importance of assessing local habitat features to successfully predict the occupancy of reptile species in urban habitats, and present directions for future research with concrete conservation and management applications.