Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine‐scale resolutions across broad‐scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field‐based habitat quality measurements and lower spatial resolution, higher spatial extent satellite‐based remote sensing. Our goal in this study was to evaluate the potential forUASstructure from motion (SfM) to estimate several dimensions of habitat quality that provide potential security from predators, and forage for pygmy rabbits (Brachylagus idahoensis) in a sagebrush steppe environment. At the plant and patch scales, we comparedUAS‐derived estimates of vegetation height, volume (estimate of food availability) and canopy cover to estimates from ground‐based terrestrial laser scanning (TLS) and field‐based measurements. Then, we mapped habitat features across two sagebrush landscapes in Idaho,USA, using point clouds derived fromUASSfM. At the individual plant scale, theUAS‐derived estimates matched those fromTLSfor height (R² = 0.85), volume (R² = 0.94) and canopy cover (R² = 0.68). However, there was less agreement with field‐based measurements of height (R² = 0.67), volume (R² = 0.31) and canopy cover (R² = 0.29). At the patch scale,UAS‐derived estimates provided a better fit to field‐based measurements (R² = 0.51–0.75) than at the plant scale. Landscape‐scale maps created fromUASwere able to distinguish structural heterogeneity between key patch types. Our work demonstrates thatUASwas able to accurately estimate habitat heterogeneity for a key terrestrial vertebrate at multiple spatial scales. Given that many of the vegetation metrics we focus on are important for a wide variety of species, our work illustrates a general remote sensing approach for mapping and monitoring fine‐resolution habitat quality across broad landscapes for use in studies of animal ecology, conservation and land management.