El Sidrón Cave is an archaeological and anthropological reference site of the Neanderthal world. It shows singular activity related to cannibalisation, and all existing processes are relevant to explain the specific behaviour of the concerned individuals. This paper presents geoarchaeological data, primarily based on mineralogical and petrographic techniques, from an investigation of the nature of the encrustations or hard coatings that affect a large part of the Neanderthal bone remains and their relationship with the depositional and post-depositional processes at the archaeological site. Crusts and patina were found to be numerous and diverse, mainly composed of calcite and siliciclastic grains, with different proportions and textures. The analysis indicated different origins and scenarios from their initial post-mortem accumulation to the final deposit recovered during the archaeological work. The presence of micromorphological features, such as clotted-peloidal micrite, needle-fibre calcite (NFC) aggregates, clay coatings, iron–manganese impregnation, and/or adhered aeolian dust may indicate that a significant proportion of the remains were affected by subaerial conditions in a relatively short period of time in a shelter, cave entrance, or shallower level of the karstic system, prior to their accumulation in the Ossuary Gallery.