Hydroxyapatite (HAp) is the main inorganic component of human bones and teeth. The doping of HAp nanocrystals plays an important role in tissue engineering, drug delivery, biomarkers and artificial bones. In this article, a postsynthetic metal ion exchange method was developed for doping hydroxyapatite (HAp) nanocrystals in organic solutions. It can be mono- or multi-ion doped with Mg²⁺, Sr²⁺, Zn²⁺, Mn²⁺, Fe³⁺ or Cu²⁺ etc., despite the significant radius variation of Ca²⁺ and doping ions. The doping ratio can be tuned in a wide range, e.g. Fe³⁺ of 0–20%, which is much higher than the ion exchange performed in aqueous solution. The structure and morphology of the HAp nanocrystals were preserved after postsynthetic doping, suggesting potential biological applications.