Incorporating trace elements into apatite coatings may permit the combination of several pharmaceutical effects due to the different ions. In this study, strontium, silicon, and fluoride ions have been incorporated into apatite coatings through a biomineralization method, which mimics an in vitro mineralization process. The surface composition was tested with X-ray diffraction and X-ray photoelectron spectroscopy, and the surface morphology was characterized with scanning electron microscopy. Compared with pure hydroxyapatite coating, the strontium, silicon, and fluoride substi-tuted apatite coatings showed different morphologies, such as spherical, needle-like, and nano-flake-like, respectively. The crystal size of these biomimetic hydroxyapatite coatings decreased after ion substitution. The results of the analysis of surface composition showed an increased amount of the ion substitutions with an increase of ion concentrations in the soaking solution. That means the ion incorporation into the apatite structure based on the biomineralization method could not only vary the ion content but also change the morphology of the apatite coatings. Herein, the role of ion sub-stitution is considered from the point of view of materials science at the micro structural and surface chemistry levels.