Abstract: Conventional continental geoarchives are rarely available in arid southern Africa. Therefore, palaeoclimate data in this area are still patchy and late Quaternary climate development is only poorly understood. In the western Kalahari, salt pans (playas, ephemeral lakes) are common and can feature quasi-continuous sedimentation. This study presents the first climate-related biomarker record using sediments from the Omongwa Pan, a Kalahari salt pan located in eastern Namibia. Our approach to reconstruct vegetation and hydrology focuses on biogeochemical bulk parameters and plant wax-derived lipid biomarkers (n-alkanes, n-alkanols, and fatty acids) and their compound-specific carbon and hydrogen isotopic compositions. The presented record reaches back to 27 ka. During the glacial, rather low δ2H values of n-alkanes and low sediment input exclude a strong influence of winter rainfall. n-Alkane and n-alkanol distributions and δ13C values of n-hentriacontane (n-C31) indicate a shift to a vegetation with a higher proportion of C4 plants at the end of the Last Glacial Maximum until the end of Heinrich Stadial I (ca. 18–14.8 ka), which we interpret to indicate an abrupt excursion to a short wetter period likely to be caused by a temporary southward shift of the Intertropical Convergence Zone. Shifts in δ2H values of n-C31 and plant wax parameters give evidence for changes to drier conditions during early Holocene. Comparison of this dataset with representative continental records from the region points to a major influence of summer rainfall at Omongwa Pan during the regarded time span and demonstrates the potential of southern African salt pans as archives for biomarker-based climate proxies.