Nanoscale materials continue to amaze researchers due to their fascinating versatile properties. One such inspiring development in nanomaterials is the design of the nanocomposite materials for multifunctional purposes from energy storage to biomedical applications. Magnetic hydroxyapatite [MHAp] nanoparticles have achieved considerable attention during the last two decades and possess exceptional prospects in the field of nanomedicine with improved multi-therapeutic approaches. The progress from controlled fabrication to advanced applications of MHAp nanocomposites is still in its infancy and few efforts have been devoted to this cause. The hybrid structure of MHAp is anticipated to be an auspicious platform for biomedical applications particularly in cancer theranostics because of good stability and biocompatibility. In this review, recent exciting features in the development of MHAp nanocomposite and promising applications in controlled drug/gene delivery and magnetic hyperthermia treatment, tissue engineering and bone regeneration, antimicrobial activity, heavy metals and toxic dyes removal, fire retardant behaviour, biosensors and the development of contrast agents for magnetic resonance imaging are highlighted and explained in detail. In addition, this study provides a comprehensive assessment of the synthesis of MHAp nanocomposites by various preparation methods, the influence of reaction parameters on the morphology and structure-property relationships based on recent studies. Finally, novel perceptions are examined regarding the ability of MHAp nanoparticles to improve hybrid nanocarriers with homogeneous structure to enhance multifunctional biomedical applications.