Bone reactivity offers a potential way to record local physical–chemical conditions prevailing in fossilization environments and archaeological sites. In the present study, a series of fossil bone samples from the karstic environments of the Bolt's Farm cave system (Cradle of Humankind, South Africa) and from fluvio‐lacustrine environments of the Tugen Hills (Gregory Rift, Kenya) is analysed. The chemical composition and infrared and nuclear magnetic resonance (NMR) spectroscopic properties of fossil samples point to a transformation of the biogenic apatite and formation of secondary apatite. Depending on the sample, the secondary apatite corresponds to a carbonate‐bearing hydroxy‐ or fluor‐apatite. The maximum fraction of secondary apatite is close to 60%, coinciding with previous observations in experimental alteration of bone in aqueous solutions and suggesting that a fraction of pristine biological apatite is likely to be preserved. The present results also suggest that the acetic acid treatment of fossil samples moderately increases their average crystallinity but may dissolve carbonate‐rich domains of secondary apatite.