Geißenklösterle Cave, located in the Ach Valley of the Swabian Alb and one of six Swabian cave sites recently named as a UNESCO World Heritage site, has a long history of archaeological research resulting in a detailed record of human occupation. Sometime around 45,000 years ago Neanderthals seemingly vanished from the Swabian landscape, and after a period of mostly geogenic deposit at Geißenklösterle Cave we find deposits containing characteristically Aurignacian artifacts dating to as early as 42,500 years ago. These Aurignacian groups brought with them complex symbolic expression and communication including bone and ivory beads, musical instruments, and animal and human figurines. This study examines the climatic context of this depopulation through a taxonomic and taphonomic analysis of the rodent and insectivore remains associated with these periods and provides a relatively unbiased climatic record for the period of ∼45,000–36,000 years ago in this region. Taphonomic analysis indicates that primarily the European eagle owl (Bubo bubo) and the kestrel (Falco tinnunculus) were responsible for accumulating the material, and allows us to quantify the potential taxonomic bias resulting from predator behaviour which includes a preference for voles, particularly the water vole (Arvicola terrestris). Additionally, rare taxa (which include species of murids and soricids) may have been present in greater quantities than our sample implies. The assemblage from Geißenklösterle Cave is dominated by the field and common vole (Microtus arvalis/agrestis), the narrow-headed vole (Microtus gregalis), and the root/tundra vole (Microtus oeconomus). Overall, the Middle Paleolithic landscape included significant woodland and forested areas while a high proportion of species restricted to cold tundra environments likely indicate punctuated cold and arid periods. The signal from the nearly geogenic layer overlying the Middle Paleolithic material includes a moderate shift in the proportion of cold tundra adapted species, suggesting that the tundra expanded leading up to the Neanderthal depopulation, but no period of drastic climatic change is recognizable. The Aurignacian was significantly colder and drier than the preceding period, with cold tundra expansion reaching its apex (for the time period studied). Based on these results the Swabian landscape first encountered by Aurignacian groups was significantly less hospitable than that known to the earlier Middle Paleolithic populations. These results correlate well with past paleoenvironmental reconstructions based on sedimentary, botanical, and faunal assemblages. There is no evidence in the small mammal record that climatic pressure drove Neanderthals from the Ach Valley, instead it seems likely they enjoyed a more temperate environment than later Aurignacian groups. Ongoing work focused on greater resolution of these climatic oscillations at similarly well-dated Swabian sites will shed further light on the timing and speed of this climatic shift and the response of the biological communities affected, including early human groups.