Humanised landscapes are causing population declines and even extinctions for some wildlife species, whereas others are adapting to the new habitat niches and resources. Synanthropy is widespread among many vertebrates, with bats a leading cause of co-habitation conflicts. However, due to a paucity of research, especially in the tropics, it is currently difficult to understand bat roosting preferences and provide building guidance to minimise these conflicts. We aimed to assess roost selection by bats in villages around Ranomafana National Park, eastern Madagascar. Ten villages were surveyed, with bats occupying 21 of the 180 sampled buildings. Of those, 17 were public buildings harbouring large molossid colonies. Bat preference was driven by the type of building, its height and a lack of fire use by the inhabitants. Colonies were mainly found under metal sheets within large chambers, whereas only isolated bats were detected in the roofs of traditional cabins. Temperatures up to 50o C were recorded inside a roost, representing the highest temperatures recorded for an African maternity roost. Molossidae bats appear to have found a suitable alternative to their native roosts in hollow, old and tall trees in pristine forests, which are becoming rare in Madagascar. This suggests that human-bat interactions in Madagascar will likely increase alongside rural development and destruction of primary forest habitats. Although beneficial ecosystem services provided by bats are well-known, several cases of colony eviction were noted, mostly due to unwanted co-habitation. Shifting to modern construction while combining traditional techniques with proper roof sealing could prevent the establishment of colonies in undesired locations whereas cohabitation conflicts could alternatively be minimized by reducing direct interaction with humans. In light of our results, we urge caution in bat evictions, and greater attention when bringing modern building practices, often supported by foreign initiatives, to poor rural communities in developing countries.