A bio-inspired mineralisation process was investigated and applied to develop novel hybrid magnetic materials by heterogeneous nucleation of Fe2+/Fe3+-doped hydroxyapatite nanocrystals onto a biopolymeric matrix made of a Type I collagen-based recombinant peptide (RCP). The effect of the synthesis temperature on the phase composition, crystallinity and magnetic properties of the nucleated inorganic phase was studied. The as-obtained magnetic materials were then engineered, by using a water-in-oil emulsification process, into hybrid magnetic microspheres, which were stabilized by de-hydrothermal treatment yielding cross-linking of the macromolecular matrix.Thorough investigation of the physicochemical, morphological and biological properties of the new hybrid microspheres, as induced by the presence of the inorganic nanophase and controlled iron substitution into hydroxyapatite lattice, revealed bone-like composition, good cytocompatibility, designed shape and size, and tailored magnetization. Such features are interesting and promising for application as new biomaterials with ability of remote activation and control by using external magnetic fields, for smart and personalized applications in medicine, particularly in bone tissue regeneration.