Fossil material from 12 caves situated in the Kraków-Częstochowa Upland (southern Poland) was studied. In 17 samples of osteological material, 8,275 individuals (Minimal Number of Individuals, MNI = 4,571) of 12 bat species were identified. Thirteen separate thanatocoenoses were found (R × C test) from which bone material was dated using the ¹⁴C AMS method; 13 dates from 6,725 to 820 ¹⁴C yr BP (yr BP) were obtained. Correspondence analysis for thanatocoenoses from the Atlantic and Subboreal periods distinguished two bat species groups and two thanatocoenosis groups: 1) pontic-mediterranean species with a higher frequency during the Atlantic period, e.g., Rhinolophus hipposideros which reoccurs more abundantly at the end of the Subboreal period and Myotis emarginatus, which is absent in earlier sediments with the exception of one episode; 2) Myotis daubentonii, Plecotus auritus, and Myotis dasycneme which increase in frequency during humid and cool periods (5,500–1,200 and 3,000–2,700 yr BP); 3) thanatocoenoses from the Holocene climatic optimum (6,000–5,500 yr BP) characterized by a dominance of Myotis nattereri; a decrease in its frequency occurred during the cooler end of the Atlantic period; 4) thanatocoenoses from the Subboreal period (4,100–3,500 yr BP) characterized by a dominance of Myotis bechsteinii. The maximum frequency of M. bechsteinii correlates with an increasing share of Fagus and Carpinus in forest ecosystems, while its decrease was probably caused by disease and was independent of human activity. Myotis myotis was found in assemblages from the Atlantic period, while the remains of a nursery colony in Nietoperzowa Cave (820 ± 25 yr BP) indicate that reproduction of this species occurred to the north of the Carpathians before the appearance of houses with attics. The presence of mass concentrations of Pipistrellus pipistrellus (s.l.) in caves was confirmed for the Subatlantic period (2,325 ± 30 yr BP), which shows its independence from both thermal balance and human influence on contemporary ecosystems. The low frequency of Barbastella barbastellus in thanatocoenoses prevents reconstructions. Reconstructions for the Atlantic and Subboreal periods show that the composition of the bat fauna depends on changes in climate and vegetation, while human activity seems to have marginal impact. A comparison of paleozoological and radiocarbon datings revealed large differences in age estimation of the thanatocoenoses.