The sandy coastal plains of Brazil are one of the most threatened ecosystems of the Atlantic Forest domain, due primarily to habitat suppression and fragmentation. Glaucomastix littoralis is a threatened endemic lizard that was found to have a declining population in a previous study. Our principal hypothesis in the present study is that altered habitats are less likely to be occupied by G. littoralis due to the elimination of conditions favorable to this species. We tested this hypothesis by analyzing which habitat variables determine abundance, occurrence, and detectability of G. littoralis, comparing populations from six different sites representing different levels of conservation in sandy coastal habitats (restinga) in northern Rio de Janeiro state. We used Royle–Nichols occupancy models to estimate the abundance of G. littoralis and single-species multi-scale occupancy models to estimate its detectability and spatial distribution. The location of the transect was the covariate that best explained the abundance of G. littoralis. The estimated population size for the whole area was 265 individuals, and the estimated mean abundance per transect was = 18 ± 3. Occupancy by G. littoralis was higher in transects with regenerating vegetation. We found a positive relationship between large-scale occupancy rates and the distance of the transect from the nearest human settlement. Detectability was affected by air temperature and was higher at sites with deeper leaf litter and in sandy microhabitats. Site occupancy by G. littoralis was also higher at sites with deeper leaf litter. Our findings indicate that the modification of Brazilian restinga habitats could drive G. littoralis to extinction.