Bone diagenesis is a complex process that modifies bone components in response to burial conditions. These modifications help to understand deposit formation and classify fossils by stratigraphy. The combined techniques of X-ray diffraction with Rietveld refinement and infrared spectroscopy were used to study the bone diagenetic processes along the complete stratigraphic sequence of Galería site (Sierra de Atapuerca, Spain). Eleven chemometric indices considering the different bone components (phosphates, carbonates, organic phase), together with the apatite unit cell parameters and cell volume were evaluated by 9 machine learning algorithms for bone diagenesis/stratigraphic classification. The results showed differences along the stratigraphic sequence due to changes in the apatite structure chemistry (i.e., F