Surface modification of orthopedic and dental implants has been demonstrated to be an effective strategy to accelerate bone healing at early implantation times. Among the different alternatives, coating implants with a layer of hydroxyapatite (HAp) is one of the most used techniques, due to its excellent biocompatibility and osteoconductive behavior. The composition and crystalline structure of HAp allow for numerous ionic substitutions that provide added value, such as antibiotic properties or osteoinduction. In this article, we will review and critically analyze the most important advances in the field of substituted hydroxyapatite coatings. In recent years substituted HAp coatings have been deposited not only on orthopedic prostheses and dental implants, but also on macroporous scaffolds, thus expanding their applications towards bone regeneration therapies. Besides, the capability of substituted HAps to immobilize proteins and growth factors by non-covalent interactions has opened new possibilities for preparing hybrid coatings that foster bone healing processes. Finally, the most important in vivo outcomes will be discussed to understand the prospects of substituted HAp coatings from a clinical point of view.