Research on plant–animal interactions has been focused on direct consumer interactions (i.e. plants as resources), but non-trophic interactions including providing shelter or interference with movement can also affect the fine-scale distribution of animals. In particular, non-trophic interactions that are positive could support threatened animal populations. Positive interactions have been used in the restoration of plant communities, but have not yet been extended to the management of animal habitat. In this study, we tested the hypothesis that non-trophic interactions influence the occurrence of an endangered lizard species in an arid shrub-annual system. At a location known to have a population of blunt-nosed leopard lizards (Gambelia sila), we geotagged 700 shrubs, measured shrub morphometric traits, collected biomass samples, and surveyed for lizard presence using scat detection dogs over two years. Relative to 2014, in 2013 plant productivity was high and lizard scats were found more frequently in areas with low invasive grass cover (i.e. residual dry matter, RDM). In 2014, plant productivity was low because of an extreme drought year, and lizard scats were more frequently observed under shrub canopies, particularly those with relatively dense cover. These findings support the novel theory that positive non-trophic interactions are a critical form of plant–animal interactions in addition to consumption. Dominant shrubs can act as a foundation species by functioning as a basal node in structuring both plant and animal communities through a network of interactions. Managing dominant plants, in addition to habitat, is therefore important for conserving animal species in arid ecosystems.