The Cueva Mayor karst system of Atapuerca, in Northern Spain, hosts a highly significant record of human occupation from the Pleistocene. The climatic context of the human activities during the Pleistocene-Holocene for this inland site has not been well constrained, since existing records of the palaeoclimatic evolution of the Northern Iberian Peninsula are from more distal coastal and high-elevation sites. In this study, we interpret the palaeoenvironmental information recorded on the petrography of a stalagmite and the pollen spectra of the Sierra de Atapuerca karst system during the last 20 kyr. The integration of both types of records has allowed us to define four palaeoenvironmental stages. During the Upper Pleistocene and until 12.8 kyr BP, the climate was cold and dry, toward the end of the interval evolving to wetter and warmer conditions. From 12.8 to 7.7 kyr BP, during the Mesolithic-Neolithic, a major erosion event in both records marks the Pleistocene-Holocene transition. Around 5.9 kyr BP, the Late Neolithic, environmental conditions indicate a climatic optimum with a marked seasonality. The environmental conditions became drier from 4.2 kyr BP until the present, with a decrease in the woodlands. This aridity signal might be amplified by the impact of a more intense human agricultural activity after 3.1 kyr BP, during the Bronze Age.