Research and media attention is disproportionately focused on taxa and ecosystems perceived as charismatic, while other systems with high levels of endemism, are often under-protected and overlooked such as caves and subterranean ecosystems. Yet these more challenging systems are also threatened, with karsts for example losing around 6% of their area each year, highlighting the urgent need for protection, especially as up to 90% of cave endemic species may be undescribed. Bats are keystone to cave ecosystems making them potential surrogates to understand cave diversity patterns and assay conservation priorities. Almost half (48%) of known bat species use caves for parts of their life histories, with 32% endemic to a single country, and 15% currently threatened. We combine global analysis of cave bats from the IUCN with site specific analysis of 1930 bat caves from 46 countries to develop global priorities for the conservation of the most vulnerable cave ecosystems. Globally, 28% of caves showed high diversity and were highly threatened and 4% had high diversity but not currently threatened. Amongst regions, the highest concentration of conservation priority caves were in the Palearctic, and tropical regions except the Afrotropics, which requires more intensive data sampling. Our results further highlight the importance of prioritising bat caves using locally collected data, and parameter selection is optimised (i.e., appropriate landscape features and threats). Finally, to protect and conserve these ecosystems it is crucial that we identify priorities in species and habitat-level, and map vulnerable habitats with the highest biodiversity and distinctiveness.