Habitat restoration is typically focused on reestablishing suitable conditions at a local scale, but landscape constraints may be important for keystone species with limited dispersal. We tested for time lags and examined the relative importance of local and landscape constraints on the response of the banner-tailed kangaroo rat (Dipodomys spectabilis) to restoration of Chihuahuan Desert grasslands in New Mexico, USA. Dipodomys spectabilis is a keystone species that creates habitat heterogeneity and modifies the structure of plant and animal communities. We selected 21 sites and compared density of D. spectabilis between areas treated with herbicide to control shrubs (treated areas) and paired untreated areas. We evaluated whether density of D. spectabilis depended on treatment age, local habitat quality (vegetation and soil structure), and landscape factors (treatment area and spatial connectivity). Density was greater at treated areas than at untreated areas due to a direct effect of reduced shrub cover. However, the response of D. spectabilis to restoration was lagged by a decade or more. Structural equation modeling indicated the time lag reflected a dispersal constraint as opposed to a temporal change in habitat quality. This inference was corroborated by a positive relationship between density at treated areas and connectivity to source populations. Our results indicate that density of D. spectabilis depended strongly on the spatial configuration of treated areas, which supports a landscape mosaic approach to restoration. If keystone species commonly exhibit limited dispersal ability, landscape constraints may be broadly important for shaping ecosystem structure and function after habitat restoration.