The Brazilian savanna (Cerrado) is a biodiversity hotspot with high deforestation rates that lead to extensive habitat changes, especially around protected areas (PAs). In our study, we analyzed how bats are affected by habitat changes comparing assemblages inside and outside Cerrado PAs. We compared diversity patterns of bats in relation to species composition, number of captured bats, as well as body condition and reproductive condition in cerrado sensu stricto (s.s.) and gallery forests. From September 2007 to June 2008, we captured 495 bats belonging to 25 species, 4 families, and 6 foraging guilds. When comparing captured bats inside and outside PAs, we found different patterns for both habitats, but with no differences in species richness for both habitats in relation to habitat perturbation. In relation to the degree of preservation, bat assemblages tend to be dissimilar between cerrado s.s. and similar between gallery forests. Besides that, in cerrados s.s., bats are less captured, or negatively affected, by habitat disturbance outside PAs; while in gallery forests, they are positively affected. Likewise, some bat species in gallery forests present higher body condition and more reproductive individuals outside PAs. Finally, we suggest that the intense habitat change in cerrado s.s. does cause negative effects on bats, while the positive effects found in degraded gallery forests may be due to the higher resource availability derived mainly from pioneer plants. Therefore, the presence of both nectarivorous bats in cerrado s.s. and frugivorous bats in gallery forests can be considered good indicators for habitat disturbance.