Tissue engineering (TE) represents a valid alternative to traditional surgical therapies for the management of bone defects that do not regenerate spontaneously. Scaffolds, one of the most important component of TE strategy, should be biocompatible, bioactive, osteoconductive, and osteoinductive. The aim of this study was to evaluate the biological properties and bone regeneration ability of a porous poly(ɛ-caprolactone) (PCL) scaffold, incorporating MgCO3 -doped hydroxyapatite particles, uncoated (PCL_MgCHA) or coated by apatite-like crystals via biomimetic treatment (PCL_MgCHAB). It was observed that both scaffolds are not cytotoxic and, even if cell viability was similar on both scaffolds, PCL_MgCHAB showed higher alkaline phosphatase and collagen I (COLL I) production at day 7. PCL_MgCHA induced more tumor necrosis factor-α release than PCL_MgCHAB, while osteocalcin was produced less by both scaffolds up to 7 days and no significant differences were observed for transforming growth factor-β synthesis. The percentage of new bone trabeculae growth in wide defects carried out in rabbit femoral distal epiphyses was significantly higher in PCL_MgCHAB in comparison with PCL_MgCHA at 4 weeks and even more at 12 weeks after implantation. This study highlighted the role of a biomimetic composite scaffold in bone regeneration and lays the foundations for its future employment in the clinical practice.