Fossils of megaherbivores from eight late Pleistocene 14C- and OSL-dated doline infillings of Ajoie (NW Switzerland) were discovered along the Transjurane highway in the Swiss Jura. Carbon and oxygen analyses of enamel were performed on forty-six teeth of large mammals (Equus germanicus, Mammuthus primigenius, Coelodonta antiquitatis, and Bison priscus), coming from one doline in Boncourt (~ 80 ka, marine oxygen isotope stage MIS5a) and seven in Courtedoux (51–27 ka, late MIS3), in order to reconstruct the paleoclimatic and paleoenvironmental conditions of the region. Similar enamel δ13C values for both periods, ranging from − 14.5 to − 9.2‰, indicate that the megaherbivores lived in a C3 plant-dominated environment. Enamel δ18OPO4 values range from 10.9 to 16.3‰ with a mean of 13.5 ± 1.0‰ (n = 46). Mean air temperatures (MATs) were inferred using species-specific δ18OPO4–δ18OH2O-calibrations for modern mammals and a present-day precipitation δ18OH2O-MAT relation for Switzerland. Similar average MATs of 6.6 ± 3.6°C for the deposits dated to ~ 80 ka and 6.5 ± 3.3°C for those dated to the interval 51–27 ka were estimated. This suggests that these mammals in the Ajoie area lived in mild periods of the late Pleistocene with MATs only about 2.5°C lower than modern-day temperatures.