Umhlatuzana rockshelter is an archaeological site with an occupational record covering the Middle Stone Age, Later Stone Age, and Iron Age. The presence of both Middle and Later Stone Age assemblages makes Umhlatuzana the ideal location for the study of the MSA–LSA transition (20–40 ka) in southern Africa. This transitional period is characterized by important modifications in stone tool technology, from prepared core technology to a toolkit based on microlith production. These changes are argued to have occurred in response to changes in climate and environment leading up to the Last Glacial Maximum. The deposits bearing the transitional assemblages at Umhlatuzana rockshelter appear homogeneous with no visible stratigraphic boundaries. This study integrates geoarchaeological techniques in order to explore fine-resolution geochemical differentiations of the sediments that are macroscopically invisible, and that will provide insight into (post-)depositional processes over time. Samples were systematically retrieved from the western profile of the site following a grid-based sampling strategy and analyzed for pH, elemental composition (XRF), and Magnetic Susceptibility. Additionally, the results were integrated with preliminary micromorphological observations. Our study reveals a steady, gradual change in the geochemistry of the deposits throughout the Pleistocene, related to a combination of environmental change and occupation intensity. We suggest that the part of the sequence reported to bear Middle to Later Stone Age transitional industries is characterized by wetter environmental conditions compared to the underlying deposits. Additionally, we support results from previous studies that excluded large scale post-depositional movement of the sedimentary sequence. Our study offers a successful multi-proxy approach to systematically sample and study archaeological deposits at the macro and micro scale, integrating a variety of geoarchaeological techniques. The approach provides insight into the depositional and post-depositional history of the site, and allows for questions of stratigraphic integrity, anthropogenic input, preservation, and environmental change to be addressed.