Research and conservation interventions are disproportionately focused on taxa perceived as charismatic, while other systems with high levels of endemism, and often under-protected such as caves and subterranean ecosystems remain neglected. Bats are keystone to cave ecosystems making them ideal surrogates to understand diversity patterns and assay conservation priorities. Using a novel framework, we assessed and mapped the global bat cave vulnerabilities and priorities at the biome and site level. Almost half (N = 678, 48%) of bat species across the world regularly use caves, with 32% endemic to a single country, and 15% currently threatened with extinction. Tropical realms and small-ranged species faced the highest levels of risk. Our analyses consistently showed that most caves with lower threat levels show higher cave biotic potential (i.e., evolutionary distinctiveness and endemism), though this may be due to the loss of species from more disturbed caves. We estimate that 3% to 28% are high-priority caves for conservation in broad-scale (biome level) and fine-scale (site-dependent) analyses respectively. Amongst regions, the highest concentration of conservation priority areas are in the Palearctic and tropical regions (except Afrotropical), which requires more intensive data sampling. Our results further highlight the importance of prioritising bat caves at local scales but show that broader scale analysis is possible if robust cave data is present and effective parameters are included (i.e., appropriate landscape features and threats). Developing priorities for these systems requires more systematic approaches as a standard measure to develop the priorities needed to maintain cave diversity.