Fluctuating asymmetry, the non-directional deviation from bilateral symmetry resulting from developmental instability, can indicate early-life environmental stress. While fluctuating asymmetry can affect individual survival and reproductive success, its effect on fitness differs between species. Here, we analyzed up to 27 years of mark-recapture data from 894 RFID tagged individuals of three forest-living bat species in southern Germany to investigate the degree of fluctuating asymmetry in forearm length. In Bechstein’s bats, Myotis bechsteinii, the species with the highest sample size, we furthermore investigated if fluctuating asymmetry has become more frequent over the study period, a time when juvenile bats have grown larger forearms in response to warmer summers. We also investigated whether fluctuating asymmetry affects individual lifespan and lifetime reproductive success in female Myotis bechsteinii. The degree of fluctuating asymmetry clearly exceeding the measurement error estimated on recaptured individuals was similar in all three species (1.8%). In female Myotis bechsteinii, the frequency of fluctuating asymmetry did not increase over the course of the study and even strong asymmetry had no effect on individual reproductive success and life expectancy. Our data suggest that fluctuating asymmetry is a poor predictor of fitness in the female Myotis bechsteinii studied, and is so far unaffected by the warming environment which is leading to larger individuals in our study population.