With a rich, well-dated Early Upper Palaeolithic layer, the Mughr el-Hamamah cave site is key for understanding the Middle-Upper Palaeolithic transition in the Levant. The archaeological deposit consists of two units. Layer A resulted from pastoral activities during the 20th century and Layer B dated between 44.5 and 40.0 ky BP. During Layer A’s formation, shepherds disturbed Layer B, redepositing Early Upper Palaeolithic sediments and lithic artefacts in Layer A matrix. Activity from Layer A’s formation also resulted in spatially patchy percolation and bioturbation, leaving microarchaeological traces such as dung spherulites in some areas in Layer B. In contrast, contemporaneous chemical diagenetic processes from Layer B’s primary formation caused spatially uneven post-depositional dissolution of animal bone. In this article we present a multi-proxy microarchaeological approach to investigate the post-depositional processes in Layer B, focussing on possible impacts on the plant archaeological record. The identification of intrusive spherulites from shepherds’ activities define the limits of disturbance in Layer B. Micromorphological analyses have identified four intact micro-facies in Layer B, representing an interplay of natural and anthropogenic factors. Micromorphological details in bedded combustion features favour the interpretation that associated phytoliths represent fuel traces. Dicot fruit phytoliths occur in the western area of the cave, where well-preserved charred wood and seeds were also found. Grass-diagnostic phytoliths correspond to C3 and C4 taxa, indicating an overall humid environment with dry spells. Microarchaeological analysis identifies traces of both bedded and dispersed hearth materials, mixed with variable plant resources for food, fuel, and possibly other uses. This strengthens the interpretation of Mughr el-Hamamah Layer B as a dense, complicated palimpsest of recurring activities, formed over many millennia.