Several ochre-rich sediment samples, dating back to approximately 60 ka, from the Howiesons Poort layers at Klipdrift Shelter, South Africa, were analyzed using palaeoproteomics. The objective was to investigate the presence of protein residues to understand better the function and significance of ochre-bearing surfaces within the Middle Stone Age context of southern Africa. Our analysis identified type I collagen proteins matching those of the common eland (Taurotragus oryx) in two samples. These findings, considered alongside existing evidence of pigment use, suggest that mixing eland-derived proteins with ochre may have served both practical and symbolic purposes. To our knowledge, this study represents one of the earliest efforts to recover ancient proteins from legacy sediment samples and to explore the association between ochre and animal-derived biomolecules in deep prehistory.