Of the 181 Brazilian bat species (Mammalia: Chiroptera), 46,7% occur in urban areas. However, little is known about the influence of these environments on species’ ecology, and few studies about urban bat community structure in Brazil have been published to date. The urbanization process, however, potentially lead to critical ecological changes in bat communities’ intra and interspecific pathogenic transmissions dynamics. Conversely, few published papers detected pathogens in urban bats. The present work aimed to perform bat captures in a preserved-rural-urban gradient from 2021 to 2022 to investigate how urbanization influences their richness, relative abundance, and activity degree. Most captured bats were Phyllostomidae, especially Sturnira lillium, Artibeus lituratus, A. fimbriatus, Glossophaga soricina, and Platyrrhinus lineatus, among others. From preserved-rural towards urban areas the lesser the bat richness, the higher the relative abundance of the captured bats. Noise level, luminosity and relative humidity correlated with bat abundance. The proportion of genders, sexually active bats and their size (weight, right forearm length, and body mass index) were stable throughout the investigation. Still, the proportion of pregnant females was higher in Spring and the number of juveniles in Summer, evidencing the seasonality of reproduction. No viruses (rabies and coronavirus), Salmonella spp. and Leptospira spp. were detected in the sample. Still, several Enterobacteria were isolated, evidencing a significant role of bats in the circulation of pathogens of medical and veterinary interest. These results are crucial in the pursuit of an harmonious coexistence between humans, bats and domestic animals in areas with different levels of anthropization.