Especially in the temperate zone, female bats are exposed to increased energy demands during gestation. In addition, abiotic factors, such as ambient temperature and pathogen load, can significantly affect reproduction success. Bats are considered natural reservoirs for a wide variety of pathogenic agents, and have developed strong immune systems to cope. Nevertheless, very little is known about the influence of these pathogenic microorganisms on bat health as most infections are asymptomatic. In this study, we monitored presence of non-tuberculous mycobacteria (NTM) in female common noctule bats Nyctalus noctula during gestation. Eight NTM species, subspecies or complexes (Risk Group 1: Mycobacterium hiberniae and M. terrae complex; Risk Group 2: M. arupense, M. avium ssp. hominissuis, M. fortuitum, M. interjectum, M. peregrinum, M. septicum) were confirmed as part of the female gut microbiome during gestation, with representation changing during foetal development. Following hibernation, most females were infected, though infection load and severity were relatively low. Just prior to parturition, however, a high proportion of females were infected with a high, often pathogenic, NTM load. Females who gave birth to twins had a higher (though non-significant) proportion of positive samples after hibernation and before parturition. Negative correlations between two consecutive measurements suggest that female N. noctula can cope with NTM loading, even during energy-demanding pregnancies. Bat faeces appear to be a source of numerous NTM species and, as such, bats can be considered as vectors for NTM spread in the environment.