Conifer encroachment in sagebrush ecosystems reduces habitat heterogeneity, niche space, and resource availability, all of which negatively affect many wildlife populations. Sagebrush restoration is recommended as a management action to mitigate conifer encroachment and restore wildlife across millions of hectares in the Great Basin. Despite this recommendation, the effects of conifer encroachment and sagebrush restoration are unknown for most wildlife species. Small nonvolant mammal communities include keystone species, consumers and prey; facilitate energy flow and ecological function; and provide important ecological goods and services. We assessed causal relationships between conifer encroachment and sagebrush restoration (conifer removal and seeding native plants) on small mammal communities over 11 yr using a Before-After-Control–Impact design. Sagebrush habitat supported an additional small mammal species, twice the biomass, and nearly three times higher densities than conifer-encroached habitat. Sagebrush restoration increased shrub cover, decreased tree cover, and density but failed to increase native herbaceous plant density. Restoration caused a large increase in the non-native, invasive annual cheatgrass (Bromus tectorum L.). Counter to prediction, small mammal diversity did not increase in response to sagebrush restoration, but restoration maintained small mammal density in the face of ongoing conifer encroachment. Piñon mice (Peromyscus truei), woodland specialists with highest densities in conifer-encroached habitat, were negatively affected by sagebrush restoration. Increasing cheatgrass due to sagebrush restoration may not negatively impact small mammal diversity, provided cheatgrass density and cover do not progress to a monoculture and native vegetation is maintained. The consequences of conifer encroachment, a long-term, slow-acting impact, far outweigh the impacts of sagebrush restoration, a short-term, high-intensity impact, on small mammal diversity. Given the ecological importance of small mammals, maintenance of small mammal density is a desirable outcome for sagebrush restoration.