Conservation of poorly known species is challenging as lack of knowledge on their specific requirements may hamper effective strategies. Here, by integrating biogeographical and landscape analyses, we show that informed actions can be delineated for species with limited presence-only data available. We combine species distribution and connectivity models with temporal land cover changes to define priority areas for conservation of the endemic Brazilian three-banded armadillo, one of the most threatened xenarthrans that was once considered extinct in the wild. We revealed that areas of savanna and grassland are the most suitable habitats for the species and that uplands in the Caatinga ecoregion have a greater likelihood for dispersal. The few remnant armadillo populations are spatially associated with core areas of natural vegetation remnants. Worrisomely, 76% of natural core areas were lost in the past 30 years, mirroring the species’ severe population decline. Preserving the remnant core natural areas should be a high priority to ensure the species’ survival. We highlight key areas for proactive and reactive conservation actions for the three-banded armadillo that will benefit other threatened sympatric species. Our integrative framework provides a set of valuable information for guided conservation management that can be replicated for other poorly known species.