As an apex predator, habitat selection by African lions, Panthera leo, is primarily determined by bottom-up processes; however, increasing anthropogenic pressures may alter these relationships. Using camera traps and track surveys in the Limpopo National Park, Mozambique, we collected detection/non-detection data of lions and their prey and combined these with occurrence data on bushmeat poaching activities and spatial data on agro-pastoralist land use and other landscape features. We used hierarchical modelling within an occupancy framework to determine the relative influences of ecological variables on resource use and non-use by lions at two spatial scales. Habitat use by lions was most strongly influenced by the occurrence of their preferred prey across both spatial scales. However, lions were strongly negatively predicted by bushmeat poaching at the finer spatial scale and generally negatively predicted by agro-pastoralist activities at the coarser scale. Restricting our analysis to the home-range scale would have greatly underestimated the impact of bushmeat poaching on the ecology of lions. The results of our study illustrate the trophic dependency of prey resources to lions and the importance of considering scale when investigating species habitat use. Importantly, our study also demonstrates the limiting influence of bushmeat poaching on the use of habitat by an apex predator.