The Holocene has always been considered a crucial epoch where the major cultural steps of humankind took place. Understanding past Holocene climatic variability, shifts in vegetation, and faunal communities are among crucial challenges in predicting the upcoming changes of the natural environment. In Central Europe, the Kraków-Częstochowa Upland is one of the best study areas for detecting faunal, environmental, and climate shifts. For that reason, we choose to study the small vertebrate and mollusc communities of three archaeological sites with Holocene horizons: Sąspowska Zachodnia Cave, Ciasna Cave, and Małe Rockshelter. We analysed the faunal community shifts, and we compared our results with the major Holocene sites in the area with the correspondence and cluster analyses. The environment and climate were reconstructed through Habitat Weighting, Quantified Ecology, malacological spectra and Bioclimatic methods. Environment and climate values showed a temporary replacement of the Late Glacial tundra and grasslands with boreal forest mixed with open wetlands during the Preboreal and then stable landscapes dominated by temperate forests. Models based on rodent data show that temperature and precipitation generally increased, starting from the Boreal, to reach values near, or sometimes overwhelm, the current climate values of the area during the Atlantic and Subboreal. The climate values obtained from herpetofaunal analyses show very slight changes between the Preboreal and the Atlantic (Ciasna Cave layers 3 and 4), except for the winter temperatures, whereas results obtained for Sąspowska Zachodnia Cave are probably biased by a very low number of recovered remains. Among rodents, a major negative oscillation detected in layers related to the edge of Early Holocene was related to the Preboreal Oscillation or long-lasting effect of the Younger Dryas.