Hydroxyapatite is the main mineral component of bones and teeth. Fluorapatite, a bioceramic that can be obtained from hydroxyapatite by chemical substitution of the hydroxide ions with fluoride, exhibits lower mineral solubility and larger mechanical strength. Despite the widespread use of fluoride against caries, a reliable technique for unambiguous assessment of fluoridation in in vitro tests is still lacking. Here we present a method to probe fluorapatite formation in fluoridated hydroxyapatite by combining Raman scattering with thermal annealing. In synthetic minerals, we found that effectively fluoride substituted hydroxyapatite transforms into fluorapatite only after heat treatment, due to the high activation energy for this first order phase transition.