Plasma sprayed coatings composed of stoichiometric hydroxyapatite have been extensively used to improve integration of metallic implants in the host bone, as hydroxyapatite (HA) is normally regarded as similar to the mineralized phase of bone. However, these coatings exhibited several drawbacks that limited their success. On the one hand biological apatite is a carbonated-HA, containing significant amounts of foreign ions, having low crystallinity and a small crystals size. This means that it differs from stoichiometric HA in terms of composition, stoichiometry, crystallinity degree, crystal size/morphology and, as a direct consequence, solubility, and ions release in the peri-implant environment. On the other hand, thick plasma sprayed coatings can undergo cracking and delamination and are scarcely uniform. For these reasons, research is pushing into two directions: (i) Increasing the similarity of apatite coatings to real bone, and (ii) exploring deposition by alternative plasma assisted techniques, allowing to achieve thin films, and having superior adhesion and a better control over the coating composition. In this article, we review the latest advances in the field of plasma-assisted deposition of ion-substituted hydroxyapatite thin films, highlighting the state of the art, the limitations, potentialities, open challenges, and the future scenarios for their application.