Despite representing one around fifth of the world’s mammal species bats face an uncertain future. Habitat clearance, human activities, invasive species, and climate change have all been implicated as contributors to bat decline. Teasing apart the discrete impacts of these factors is critical for developing appropriately targeted recovery strategies. Long-term data revealing patterns of bat community dynamics prior to human influence are needed to separate natural and anthropogenic impacts. Here I present evidence from Quaternary fossil deposits at Naracoorte in South Australia that shows continuous habitation of caves by the Critically Endangered southern bent-wing bat (Miniopterus orianae bassanii) over at least the past 300,000 years; spanning considerable periods of climate variability. The use of particular caves as maternity or wintering sites has been consistent over this time, and mirrors precisely the patterns of cave use seen at Naracoorte today. This suggests that while the bats have been resilient to long-term change over multiple glacial cycles, the availability of appropriate cave habitat is critical. In some caves, within-cave environmental conditions are influenced by surface climate. Projected temperature increases with anthropogenic climate change may render some currently inhabited caves unsuitable. Modern habitat fragmentation and human impact on many caves has severely limited the capacity of this species to expand or contract its range in response to future climate change. Population monitoring and localised habitat restoration measures may not be enough to prevent extinction of this species. The emerging field of palaeo-conservation may provide a useful tool for planning conservation efforts.