FTIR and soil micromorphology were applied to selected sediments from the archaeological deposit of Esquilleu Cave, a late Middle Palaeolithic site in Cantabria, Spain. The main goal was to assess the integrity of the archaeological record before continuing with further excavation and research at the site. Field observations and previous sedimentological studies point to diagenetic alteration of part of the deposit, but the extent and precise nature of such processes had not been established. The results show that the upper layers are composed of fresh elements and have not undergone diagenetic transformations, although their components have been physically disturbed by cryoturbation. The rest of the deposit is well preserved with mild phosphatization due to partial dissolution of bone and calcitic ash contained in the sediment, and compression from trampling. Further excavation is necessary to have a more complete picture of the taphonomic processes taking place at the site.