Magnetic nanoparticles (MNPs) have been extensively investigated in a wide range of biomedical applications. Controlled coating of the MNPs is commonly utilized to protect and maintain their magnetic properties and to improve their biocompatibility, hydrophilicity, colloidal stability and overall biodistribution. Hydroxyapatite (HAp), a highly biocompatible material, is considered for the functionalization of MNPs. In this study, two simple chemical approaches are used to prepare nanohybrid MNPs‐on‐HAp and HAp‐on‐MNPs composites. The effect of heat treatment on the phase composition, morphology, and magnetic properties of both types of magnetic composites is extensively evaluated. In the presence of HAp, MNPs are segregated onto their surfaces and their transformation to hematite upon heat treatment is delayed. On the other hand, needle‐shaped HAp nanocrystallites preferentially grow onto the hydroxylated MNPs surfaces, leading to a synergistic enhancement in the magnetic properties of the produced nanocomposites, with preserved magnetic properties. Compared with a saturation magnetization (Ms) value of 80 emu g−1 of pure MNPs, a MNPs‐on HAp nanohybrid shows a maximum of 14 emu g−1, while nanohybrids based on HAp‐on‐MNPs show Ms values in the range of 43–78 emu g−1. These findings demonstrate the ability to fine‐tune the magnetic properties of the HAp/MNPs nanohybrids via optimizing their processing conditions.