Flotation mechanisms of calcareous phosphates ores, and in particular the reaction between phosphoric acid and fluorapatite have still to be elucidated. In the present work, variations of carbonated hydroxyfluorapatite (C-HFAp) in contact with various concentrations of phosphoric acid were studied using ex-situ and in-situ techniques, namely Raman and Infrared spectroscopy, X-Ray diffraction (XRD) and Scanning Electron microscopy (SEM). Raman spectra showed a calcium carbonate peak (CaCO3) (1085 cm−1) at low acid concentrations (between 10−3 and 10−2 mol.L−1), disappearing at higher concentrations. Similarly, kinetic studies showed that, even if CaCO3 appeared after 2 min reaction, it disappeared after 3 min. IR spectra and diffractograms seemed to display the presence of CaCO3 at low acid concentrations (peak at 713 cm−1 on the IR spectra), with a change in CaCO3 crystallinity and in the C-HFAp surface with increasing acid concentrations (broadening of the peak). Our results highlight the conversion of hydroxyfluoroapatite at high acid concentrations, with a coating of the mineral surface which prevents the dissolution of the mineral and can impact the adsorption of collectors. Our work contributes to the understanding of the mechanisms of depression of apatite minerals in phosphate ores flotation.