The study of cold-adapted faunas in Iberia is of great interest to palaeontologists because this peninsula represents the southernmost limit of the distribution in Western Europe of species such as mammoth, reindeer and woolly rhinoceros. Additionally, the direct dating of these palaeontological assemblages can provide important information regarding the palaeoecology of Palaeolithic humans. In this study, we examine the fossil assemblage recovered from the floor of the Baio cave (Zestoa, northern Iberia), which includes the remains of cold-adapted species. This site has yielded an assemblage that includes herbivores, carnivores and a small number of rodents. Our radiocarbon dating of the remains of a reindeer and a red deer yielded chronologies consistent with the Châtelperronian and Late Aurignacian occupations in the area, indicating a diachronic accumulation. Taphonomic observations suggest carnivores as being the main accumulation agents, with a minimal human contribution, along with the probable accumulation of some remains due to natural causes and/or the cave acting as a natural trap. This new evidence contributes to the existing records from other sites, such as Ekain and Mainea, suggesting severe climatic pulses during the transition from the Middle to the Upper Palaeolithic, which coincides with a complex pattern of Neandertal extinction and their replacement by modern humans.