Species with specific roosting, foraging or breeding requirements are particularly vulnerable to habitat loss and degradation. For bats, the availability and environmental condition of caves can be a limiting factor. The cave specialist Natalus macrourus (formerly Natalus espiritosantensis) is categorized as Near Threatened on the IUCN Red List but as Vulnerable in Brazil, based on a projected population reduction and a decline in its area of occupancy, extent of occurrence and/or quality of habitat. There is a lack of knowledge about the species’ distribution, natural history and ecology, information that is required for conservation. Using new occurrence data and potential distribution modelling we evaluated the distribution of N. macrourus in Brazil, analysed pressures on and threats to the species, and assessed the species’ conservation needs. Natalus macrourus is positively associated with areas with higher probability of cave occurrence and negatively associated with areas of high variation in mean daily temperature and mean annual rainfall. Areas with high environmental suitability for N. macrourus correspond to only 3% of the potential distribution modelled. We estimate that the species has already lost 54% of its natural habitat and that there is < 35% of habitat remaining in areas with high environmental suitability. We calculated that approximately half of the caves in areas with high environmental suitability are < 5 km from mining operations and only 4% of the species’ potential distribution lies within protected areas. Given the strong association of N. macrourus with caves, it is important to protect these habitats, and we recommend that caves where the species is present should receive immediate protection.