Seasonal movements between the summer and winter areas are a widespread phenomenon in bats So far, most information on the migration ecology of bats has been obtained by studies in terrestrial habitats, whereas scientific knowledge on migration over sea is scarce. We performed continuous ultrasonic acoustic monitoring at 13 locations in the southern North Sea during four consecutive years (2017–2020) and analysed the spatiotemporal occurrence of Nathusius’ pipistrelle Pipistrellus nathusii during autumn migration in relation to weather parameters and lunar phase. Our analysis showed that the main autumn migration of Nathusius’ pipistrelle at the southern North Sea occurs from mid-August until late October and most bats within the study area occur off the Noord Holland coast. North Sea crossings frequently last longer than one night; the day is spent roosting at an offshore structure. The strongest migration occurs during nights with tailwinds from the east-northeast, but bats are also recorded offshore with low to moderate headwinds or crosswinds. Bat presence decreased between the full moon and the last quarter and increased just before the new moon. Finally, our observations show that the occurrence of bats at sea was reduced in 2020 in comparison to the previous years. The results of this study show clear spatiotemporal patterns of migratory bat occurrence at the southern North Sea. The spatial distribution can be used in spatial planning of future offshore wind farms, whereas the temporal occurrence and environmental factors that shape offshore migration can be used to develop mitigation measures to reduce the number of bat fatalities.