Diagenetic alteration may limit the potential use of the biogenic composition of fossil bone as a reliable source of information for dietary, environmental and climatic reconstructions. One of the key parameters used to determine the state of preservation of fossil remains is their crystallinity. This can be evaluated by means of infrared spectroscopy, measuring the “splitting factor” (IRSF). However, the crystallinity may fail to describe the extent of chemical and mineralogical changes occurring during fossilization, and cannot be used alone as a reliable indicator of biogenic signal preservation. In this study, modern bones were experimentally heated in order to monitor the changes of FTIR spectral features related to an evolution of mineral properties. Further spectroscopic proxies of the mineral composition and structure were defined and calibrated. This method was then applied on unburnt, charred and calcined bones coming from three archaeological sites (Bize-Tournal, Organc 3 and Song Terus). The results obtained on modern and fossil bones demonstrate that low temperature heating and diagenetic processes may induce similar effects on bone mineral, while these processes are clearly distinct from those occurring during high temperature heating (>550 °C). The comparison between charred and calcined fossil bones shows that heating over 550 °C reduces the reactivity of the mineral phase and prevents compositional and structural characteristics from experiencing diagenetic modification. Applied to unburnt fossil bones, the proxies developed in this study, easily obtained from FTIR spectra, provide a more reliable evaluation of the degree of preservation than IRSF alone and contribute to a better understanding of the diagenetic processes.