Winter counts in bat hibernacula are a standard method to monitor their populations. However, it is unclear to what degree counting bats in hibernacula triggers energy consuming arousals in hibernating bats. This study quantifies the reaction of three hibernating bat species (Pipistrellus sp., Myotis nattereri, and Plecotus auritus) to a monitoring survey in a hibernaculum complex consisting of eight modified bunkers in northern Germany. Skin temperatures of hibernating bats were measured with a thermal camera at the beginning and end of each visit to quantify the proportion of individuals that elevated their body temperatures during the visit. Moreover, bat activity was recorded using light barriers placed at the entrances of the hibernacula. According to the thermal camera measurements, eight of 1,849 individuals in Pipistrellus spp. (0.4%) and one of 47 individuals of M. nattereri (2.1%) elevated their body temperature during the monitoring. The median number of light barrier passes similarly increased slightly from seven to nine on monitoring days compared to control days. Notably, general linear models suggest that the effect of monitoring was less severe with rising ambient temperatures. Our results suggest that bat monitoring in hibernacula is unlikely to threaten winter survival in hibernating bats if carried out responsibly, and the number and duration of human visits are kept to a minimum.