Background: Calcium phosphate ceramics are a group of materials that have been widely used in bone regeneration, especially hydroxyapatite (HA), because of its biocompatibility and similarity to the main mineral phase component of bone tissue. However, the biological apatite has nanometric dimensions and cationic and anionic substitutions and presents low crystallinity, which differs from stoichiometric HA. Aims: The ionic substitutions in the composition of HA have been done to mimic biological apatite and improve its physicochemical characteristics. Previous studies have demonstrated that strontium-, magnesium-, zinc-, and iron-isolated substitution stimulate osteoblastic activity, as well as reduce osteoclastic activity. Materials and Methods: This study evaluated the osteogenic potential of nanostructured carbonated hydroxyapatite microspheres (cHAMs) containing 5% strontium, 5% zinc, 5% magnesium, 1% iron, and 5% manganese, after implantation in a critical size defect in the rat's calvaria. Two experimental groups were studied: cHA 37°C (nanostructured cHA, control) and cHAM 37°C (metals doped nanostructured cHA). The animals were euthanized after 1, 3, and 6 months, and the samples were histologically processed for histomorphometric analysis regarding the presence of residual biomaterial, neoformed bone, and connective tissue. Statistical Analysis: The averages found were analyzed statistically by the D'Agostino and Pearson analysis and by Kruskal–Wallis test; significant differences were observed for P