Abstract The Erňa cave, a mass winter hibernaculum and important swarming site of the common pipistrelle, Pipistrellus pipistrellus, is located in the Slovak Karst, near the Košice urban agglomeration in eastern Slovakia. Over the past two decades, the unusual behaviour of late summer or autumn accidental but abundant occurrences of this species have been observed in buildings (so-called invasions) in Košice. It has been hypothesised that these events are related to bats swarming and hibernating in the Erňa cave; however, causality has not been confirmed. We measured the relative activity of bats from the end of the breeding season through the invasions and autumn swarming prior to the onset of hibernation by recording their echolocation calls on car-based transects in order to find any spatial and temporal linkage between activity in the urban area and the swarming site. Over two years we recorded 6,253 sequences with echolocation calls of P. pipistrellus and 5,239 records of other bats along four transects totalling 7,121 km in length. Spatial pattern analysis found that the city agglomeration presented a local hotspot of the species’ activity, especially during the invasion season. Multivariate generalised additive modelling confirmed an increased density of records of P. pipistrellus between the urban area and the hibernaculum in the pre-hibernation season, whereas this pattern was not found to be consistent on the control transects near the city. Contrary to that, other bat species showed little variation in their activity between transects and seasons. The obtained results suggest that the relatively short geographical distance between the urban agglomeration and the large swarming site is likely a clue to the frequent city invasions of the species, although the role of the city as a hibernation area cannot be completely omitted.