Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.