This study assesses the use of the Tescan Integrated Mineral Analyser (TIMA) platform, which integrates scanning electron microscopy—energy dispersive spectroscopy (SEM-EDS) chemical analysis with mineral identification software, to quantitatively determine the mineralogical composition of sediments in archaeological research. Ten samples, spanning 50,000 years of sedimentation, were examined from archaeological excavation profiles in the Boodie Cave, Barrow Island, Western Australia. TIMA mineral abundance data show a gradual change from a polymineralogic quartz-rich assemblage from ~50–12 ka to a more simple carbonate-dominate assemblage from the terminal Pleistocene. This trend is consistent with a decreasing contribution of reworked terrestrial siliciclastic sediments derived from the mainland and an increase in carbonate sediments of marine derivation, as the exposed coastal plain become submerged during post-glacial sea-level rise. SEM-EDS analysis has also provided empirical data on cultural materials, mainly bone and shell fragments that similarly reflect the increasing contribution of marine fauna into the Holocene sediments. Particularly useful is the ability of mineral mapping function of the TIMA outputs to help distinguish 16 sub-units representing sections of the main nine stratigraphic units, including at least three contiguous midden events. The SEM-EDS data indicate that the redeposited sediments were derived from the overlying midden unit, with layering reflecting differential settling of mineral phases. This study demonstrates that automated mineralogy studies using TIMA can clearly aid the identification of provenance and processes within archaeological sediments and soils.