Bats regularly migrate over the North Sea, but information on the environmental conditions when this occurs is scarce. Detailed information is urgently needed on the conditions under which bats can be expected offshore, as the number of offshore windfarms that can cause fatalities amongst bats in the North Sea is increasing rapidly. We performed ultrasonic acoustic monitoring at multiple nearshore locations at sea between 2012 and 2016 for, in total, 480 monitoring nights. We modelled the offshore occurrence of Nathusius’ pipistrelle in autumn as a function of weather conditions, seasonality, and the lunar cycle using a generalized additive mixed model (GAMM). We investigated which covariates are important using backward selection based on a likelihood ratio test. Our model showed that important explanatory variables for the offshore occurrence of Nathusius’ pipistrelle are seasonality (night in year), wind speed, wind direction, and temperature. The species’ migration is strongest in early September, with east-northeasterly tailwinds, wind speeds < 5 m/s, and temperatures > 15◦C. Lunar cycle, cloud cover, atmospheric pressure, atmospheric pressure change, rain, and visibility were excluded during the model selection. These results provide valuable input to reduce bat fatalities in offshore wind farms by taking mitigation measures.