The Middle to Upper Palaeolithic transition in Western Europe is a central topic in current paleoanthropological research. Recently, Neanderthal survival during MIS 3 and the emergence of anatomically modern humans have been the focus of much discussion in Iberia. Here, we analyse the stratigraphic and contextual resolution of the S1B/497D archaeological levels from Cova Gran, in which a techno-typological discontinuity has been identified affecting raw material, knapping systems, blanks and retouched tools. Attributes such as radial reduction systems to obtain flakes for subsequent preferential modification into notches and denticulates place level S1B within the Mousterian tradition. However, in 497D, attributed to the Early Upper Palaeolithic, laminar production intermingles the extraction of blades, bladelets and flakes. Blades were transformed into burins, end scrapers and retouched blades, and bladelets into microlithic tools such as backed points and backed bladelets. These artefacts are associated with a significant assemblage of notches, denticulates and scrapers on flakes. Radiometric data places the end of the Mousterian tradition ca. 42 ka cal BP and the appearance of the Early Upper Palaeolithic ca. 39–38 ka cal BP. The geographic and temporal ascription of levels S1B and 497D stimulate discussion on Neanderthal survival at the end of MIS 3 in northeastern Iberia. Likewise, the 497D lithic assemblage is compared to other techno-complexes assigned to this chronological range: the Chatelperronian tradition assigned to Neanderthals and Protoaurignacian linked to the appearance of anatomically modern humans. The archaeological resolution and techno-typological discontinuity documented in Cova Gran are useful points of reference in analysis of the Middle-to-Upper Palaeolithic transition in northeastern Iberia, and have implications affecting the characterization of this process across Western Europe.