A mechanism for the formation and crystallization processes of bone-like apatite grown on non-stoichiometric silicocarnotite (SC) is here proposed. Single-phase SC powders and ceramics were obtained from fixed mixtures of hydroxyapatite and bioactive glass 45S5. The bioactive behavior of SC was assessed by immersion in Hank´s solution at different times.Afterward, a systematic theoretical-experimental study of the structural properties at the micro and nanoscale using TEM was performed and correlated with SEM, EDX, XRD, and Raman techniques to determine the apatite mineralization process from the SC phase. The initial stage of apatite formation from SC was identified as the hydration and further polymerization of silanol groups, resulting in a silica-based hydrogel, which plays a critical role in the ionic exchange. As a result of the adsorption of ionic species from the medium into the silica-based hydrogel, the precipitation of crystalline apatitic structures starts through the emergence of newly formed SC nanocrystals, which act as a template for the crystallization process of a substituted apatite with SC-like structure. Then, due to the polymorphism between SC and HAp structures, the apatite layer retains the SC periodic arrangement following an epitaxial-like growth mechanism. Identification of the apatite layer formation mechanism is critical to understand its physical and chemical properties, which controls the long-term dissolution/precipitation rate of bioactive materials and their performance in the biological environment.