Bones from level G in the Arago cave (Tautavel, Southern France, 450 ky) were analysed using a combination of particle induced X-ray and gamma-ray emission (PIXE and PIGME) and X-ray diffraction (XRD). Human occupation and guano production by bats introduced a large amount of phosphate into the cave and as a result a decarbonated pocket was formed in the sediment, characterized by the dissolution of clay minerals, calcite and bones, and by the precipitation of phosphate secondary minerals. The Al released by clay minerals was reprecipitated as crandallite in the few remaining bones, and as montgomeryite with traces of crandallite in the surrounding sediments. Bones within the pocket have very high levels of Al, Fe, F and Zn and often have ‘diffusive’ type U-shaped concentration profiles. These profiles show that post-mortem uptake of trace elements occurred, and thus that trace element composition has to be used with care in palaeonutritional studies but is indicative of local palaeoenvironment. This uptake is complicated by a large increase in hydroxylapatite crystallinity in Palaeolithic bones compared to modern or more recent ones, as a result of the large P influx which occurred in the Arago cave after the sediment deposition.