This paper combines a variety of physicochemical non-destructive techniques to obtain a knowledge of the chemical and mineralogical composition of the scarce fossil bones from the Húmera paleontological site (Madrid, Spain). The main classification of the samples has distinguished six colors: red, gray, blue, white, light yellow and green. μ-XRD and Raman spectroscopy have been correlated to study the structure and to distinguish between fluorapatite, chlorapatite, bioapatite and carbonated bones. The bones have further been classified in three main types. Type I includes gray, green, white, and blue samples, classified as fluorapatite and chlorapatite containing organic matter and adsorbed water. Type II, includes the red sample classified as bioapatite, showing broad Raman bands and μ-XRD peaks due to the lattice disorder created by the B-type substitutions emerging from a high matter content. Type III sample (yellow) shows a complete replacement of apatite by calcite which induce the high porosity of the sample. Diagenetic changes add further complexity to the structure of fossil bones, not only by new ionic substitutions but also in terms of biogenic or authigenic phases that form in the fossilizing bone. The multi-technique approach from a broad interdisciplinary perspective enables a better understanding of bone fossilization.