Zooarchaeological analyses from late Middle Palaeolithic (LMP) and early Upper Palaeolithic (EUP) contexts allow to examine changes in subsistence that are key in the debate about Neanderthal and anatomically modern human socio-organisational changes. However, the effects of syn-/post-depositional processes in the modification and preservation of faunal remains are sometimes overlooked. Moreover, the quantification units chosen have implications into the way in which inferences can be made from highly fragmented assemblages. To illustrate these issues, this paper addresses the analysis of the faunal assemblages assigned to the LMP and EUP documented in Cova Gran (south-eastern Pre-Pyrenees, Iberian Peninsula). We discuss the suitability of different quantification units, taxonomical composition, skeletal part representation, age at death, the state of preservation, breakage patterns, bone surface modifications, and spatial distribution of the bone assemblages from the S1B (LMP) and 497D (EUP) levels documented in Cova Gran. The important role played by syn-/post-depositional processes is discussed to assess the resolution that zooarchaeological assemblages could offer to analyse subsistence patterns and occupation dynamics in similar geo-sedimentary environments. We investigate how the spatial distribution of the remains permits observations regarding stratigraphic and contextual resolution that might overcome the limitations imposed by aggressive post-depositional processes, which bias the statistical data that can be tested in these types of assemblages. Our results suggest patterns of continuity and discontinuity in human subsistence behaviour affecting the Middle to Upper Palaeolithic transition. The results from Cova Gran provide information to facilitate discussion on the role of zooarchaeological studies in the analysis of the lifestyle of late Neanderthals and early modern humans in the Iberian south-eastern Pre-Pyrenees.