Bat species inhabit subterranean environments (e.g., caves and mines) in small areas with specific microclimatic conditions, during various periods of their life cycle. Bats can be negatively influenced by microclimatic changes within their roosts if optimal habitat patches become unavailable. Therefore, proper management solutions must be applied for the conservation of vulnerable bat populations, especially in show caves. We have pursued an ensemble species distribution modelling approach in subterranean environments to identify sensible patches for bats. Using multi-annual temperature monitoring and bat distribution surveys performed within ten caves and mines, including show caves, we modelled relevant habitat patches for five bat species. The temperature-based variables generated from this approach proved to be effective when processed via species distribution models, which generated optimal validation results, even for bats that were heavily clustered in colonies. Management measures are proposed for each show cave to help in long-time conservation of hibernation and maternity colonies. These measures include creating suitable microclimatic patches within the caves by ecological reconstruction measures, tourist management practices in relation to bats, and show cave fitting recommendations. This approach has never been performed at this scale due to the complex geostatistical challenges involving subterranean environment mapping and can be further used as best practice guidelines for future conservation projects.