The chemical and isotopic compositions of biogenic apatite are important geochemical markers, which can suffer modifications during fossilisation. Compared with modern ones, fossil apatites generally exhibit variations in carbonate content, enrichment in fluorine, incorporation of trace elements and an increase in crystallinity parameters. Detailed understanding of these transformations induced by fossilisation should help assess the preservation of geochemical records in apatites. In this contribution, we investigate the transformation of modern bone altered under controlled conditions. Modern bone samples were soaked in aqueous solutions of neutral to alkaline pH (9–10) for one and three weeks at various temperatures (20 and 70 °C) and experiments were duplicated in fluorine-free and in 10−2 M NaF solutions. Bone transformation was monitored through the modifications of chemical (F, Ca, P) and isotopic (δ13C, δ18Oc, δ18Op) composition as well as using vibrational (ATR-FTIR, Raman) and solid-state (1H, 13C, 19F) NMR spectroscopies. The observed modifications sustain a transformation mechanism through partial dissolution of biogenic apatite and precipitation of secondary apatite. This transformation occurs irrespective of the presence or absence of fluorine and leads to the formation of carbonate-bearing fluorapatite or carbonate-bearing hydroxylapatite, respectively. The fraction of secondary apatite seems to be limited to ~60%, suggesting that its formation has a protecting role against further dissolution of the primary apatite. The observation of clumped (CO32−, F−) defects in the structural B-site of some samples as well as perturbation of the isotopic compositions attest to carbonate incorporation in the secondary apatite. Although the incorporation of fluoride ions can serve as a probe revealing dissolution-recrystallization of bone, the present study also underlines the difficulty to systematically relate mineralogical transformations to an open-system behaviour in bioapatite.