The killing of large numbers of migratory bats at wind turbines is a pressing conservation problem. Even though avoidance and mitigation measures could benefit from a better knowledge of the species’ migratory habits, we lack basic information about what habitats and corridors bats use during migration. We studied the isotopic niche dimensions of three bat species that are frequently killed at wind turbines in Germany: non‐migratory Pipistrellus pipistrellus, mid‐distance migratory Nyctalus noctula, and long‐distance migratory Pipistrellus nathusii. We measured stable carbon and nitrogen isotope ratios (δ13C, δ15N) in five tissues that differed in isotopic retention time (fur, wing membrane tissue, muscle, liver, blood) to shed light on the species‐specific habitat use during the autumn migration period using standard ellipse areas (SEAc). Further, we used stable isotope ratios of non‐exchangeable hydrogen (δ2HK) in fur keratin to assess the breeding origin of bats. We inferred from isotopic composition (δ13C, δ15N) of fur keratin that isotopic niche dimensions of P. nathusii was distinct from that of N. noctula and P. pipistrellus, probably because P. nathusii was using more aquatic habitats than the other two species. Isoscape origin models supported that traveled distances before dying at wind turbines was largest for P. nathusii, intermediate for N. noctula, and shortest for P. pipistrellus. Isotopic niche dimensions calculated for each sample type separately reflected the species’ migratory behavior. Pipistrellus pipistrellus and N. noctula showed similar isotopic niche breadth across all tissue types, whereas SEAc values of P. nathusii increased in tissues with slow turnaround time. Isotopic data suggested that P. nathusii consistently used aquatic habitats throughout the autumn period, whereas N. noctula showed a stronger association with terrestrial habitats during autumn compared to the pre‐migration period.