The aim of this study was to protect the bat community and roosting sites in the Dupnisa Cave System in the Yıldız (Istranca) Mountains in Thrace, the European part of Turkey, following the opening of the caves to tourism. We investigated the seasonal population dynamics and use of the cave system by bats, carrying out 15 surveys before (2002–2003) and 38 surveys after (2004–2008) the cave system was opened to tourism. We recorded 15 species of bats; the highest numbers recorded in a single survey were 54,600 hibernating and 11,000 breeding/nursing. Different parts of the cave system are used by bats to various degrees according to season. To protect the bats and the cave system the visitor schedule took into consideration the differences in seasonal use of the caves by bats. There was a significant increase in the total number of bats recorded in the cave system after opening for tourism, possibly because the gating of two entrances helped to control visitation. The results of our surveys of this cave system show that gating of entrances and visits by tourists are not necessarily incompatible with the use of caves by bats for both hibernating and nursing. Understanding how the three caves are used seasonally by the bat community, and for what purposes (hibernation vs nursing), was critical for the establishment of an appropriate management plan for tourism.