A good understanding of species-habitat associations, or habitat use, is required to establish conservation strategies for any species. Many amphibian species are elusive and most information concerning amphibian habitat use comes from breeding sites where they are comparatively easy to find and study. Knowledge about retreat sites is extremely limited for most species and for the greater part of the year. For such species, it is especially important to factor in detection probability in habitat analyses, because otherwise distorted views about habitat preferences may result, e.g., when a species is more visible in habitat type B than in A, even though A may be preferred. The South American red-belly toad, Melanophryniscus pachyrhynus, is a range-restricted species from Southern Brazil and Uruguay that inhabits open areas with rocky outcrops and is usually seen only during explosive breeding events. Here we studied the fine-scale habitat use of the red-belly toad outside of the breeding season to identify retreat sites and test for the importance of accounting for species imperfect detection, using Bayesian occupancy models. We identified shrub density and the number of loose rocks as important predictors of occupancy, while detection probability was highest at intermediate temperatures. Considering the harsh (dry and hot) conditions of rocky outcrops, shrubs and loose rocks may both work as important refuges, besides providing food resources and protecting against predation. Rocky outcrops have been suffering changes in habitat configuration and we identify nonbreeding habitat preferences at a fine scale, which may help to promote population persistence, and highlight the importance of accounting for imperfect detection when studying secretive species.