In urban centers, sewage treatment plants (STPs) serve as foraging and shelter areas for bats; however, they are sources of persistent pollutants that affect the health of these animals. This study aimed to investigate the impact of pollutants from an STP on the health of different species of neotropical bats from different guilds using non-invasive biomarkers. A conservation unit, the Silvania National Forest (SNF), was used as a reference area for comparison purposes. Blood, buccal mucosa, and fur samples were obtained for comet assay, micronucleus test, leukocyte profile, and metal concentration analysis in fur. Our results demonstrated that bats collected at the STP show a higher frequency of genotoxic damage, nuclear abnormalities, and an inflammatory response linked to infection than bats from the SNF. Regarding guilds, frugivores and nectarivores showed more pronounced responses to damage, but insectivores bats also showed relevant responses. While STPs are considered a source of pollutants, other urban sources of contamination likely contributed to these results. Still we encourage further studies using other non-invasive biomarkers, detection analysis of different pollutants in biological matrices, and the use of other wildlife species inserted in urban centers.