Despite the lesser preservation of bat fossils compared to karstic sites, fluviolacustrine deposits are of crucial importance for assessing the local palaeodiversity of bats. This was confirmed by three faunas from the upper Miocene of Slovakia (Borský Svätý Jur, MN9; Studienka A, MN9; Krásno, MN11), which comprise seven species—Miostrellus cf. Miostrellus noctuloides (Lartet, 1851), Myotis cf. Myotis murinoides (Lartet, 1851), ‘Otonycteris’ sp. indet., Miniopterus sp. indet., Vespertilionidae gen. indet. sp. indet. 1, Vespertilionidae gen. indet. sp. indet. 2, and Rhinolophus cf. Rhinolophus grivensis Depéret, 1892. Bats represent ~ 1.40% of the small mammal remains from Borský Svätý Jur, ~ 0.25% of those from Studienka A, and ~ 1.78% of those from Krásno. The MN11 fauna from Krásno consists of six distinct species, which is unusual for a Miocene fluviolacustrine deposit. Most likely, this is the consequence of the relatively high frequency of bats in the taphocoenosis, therefore providing a more complete and more accurate picture of the Carpathian late Miocene bat faunas. This material encourages the study of fluviolacustrine deposits to unravel the cryptic diversity of Neogene taxa.