Geoarchaeological analysis of the Middle and Upper Palaeolithic record preserved in cave, rock-shelter and open-air sites in the northern sector of the Meso-Cenozoic of the Western Iberian Peninsula margin (Portugal) reveals several disconformities (erosive unconformities), hiatuses and surface stabilization phases. A recurrent disconformity, dated to ca. 29,500–32,000 cal yr BP, in the time range of Heinrich event 3, must correspond to a main erosive event related to the impacts of climate change on the landscape, including a reduction in vegetation cover and altered precipitation patterns, with the consequent accelerated down-cutting by stream systems, slope reactivation and endokarstic reorganisation, causing the erosion of sediments and soils accumulated in cave, rock-shelter and open-air sites. These processes create a preservation bias that may explain why Early Upper Palaeolithic finds in primary deposition context remains exceptional in the carbonate areas of central-western Portugal, and possibly elsewhere in the other places of Iberia. The impact of such site formation processes must therefore be duly considered in interpretations of the current patchy and scarce archaeological record of the Middle-Upper Palaeolithic transition in south-western Iberia.