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Each year, large numbers of bats move across Europe between their summer and winter areas, yet even though many of them are endangered and legally protected, we are unaware about many aspects of their migratory behaviour. Here, taking Nyctalus noctula as a model species, we used stable hydrogen isotopic values in fur (δ2Hf) as an endogenous marker to shed light on the migratory behaviour of more than 1000 bats from hibernacula across Central Europe. Specifically, we asked the following questions: How flexible is migration in temperate zone bats? Which general migration pattern do noctule bats follow? How repeatable and thus predictable is the migratory behaviour of individuals? Do morphological correlates of migration occur in bats? Our study confirmed that noctule bats engage in partial and female-biased migration across Europe, suggesting strongest migration pressures for northern populations. Further, we revealed a combination of partial and differential migration patterns with highly variable migration distances which lead to a pronounced mixing of different source populations in hibernacula where mating occurs. Most individuals were consistent in their migration strategy over time, i.e. 86% could be repeatedly assigned to either long-distance or regional origin across years. This is consistent with our finding that the between-individual component explained 84% of the variation in δ2Hf values, suggesting specialized individual migratory behaviours and a strong natal philopatry. We discovered a positive correlation between forearm length and migration distance and support for the sex-specific effects of migration on body condition. Our study elucidated migration patterns over large geographical scales, demonstrating that considerable numbers of migratory bats originating from distant populations depend on hibernacula across central Europe, calling for an international conservation management.