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While bone regenerates itself after an injury, a critical bone defect requires external interventions. Engineering approaches to restore bone provide a temporary scaffold to support the damage and provide beneficial biological cues for bone repair. Biomimetically generated scaffolds replicate the naturally occurring phenomena in bone regeneration. In this study, a gelatin-calcium phosphate nanocomposite was synthesized by an efficient and cost-effective double-diffusion biomimetic approach. Calcium and phosphate ions are impregnated in the gelatin, mimicking the natural bone mineralization process. Glutaraldehyde from 0.5 to 2 w/v% was used for gelatin cross-linking and mechanical properties of the scaffold, and its biological support for rat bone marrow mesenchymal stromal cells was analyzed. Analysis of scanning electron microscopy images of the nanocomposite scaffolds and Fourier transform infrared (FTIR) and X-ray diffraction (XRD) characterizations of these scaffolds confirmed precipitation of calcium phosphates in the gelatin. Moreover, lysozyme degradation assay showed that scaffold degradation reversely correlates with the concentration of the cross-linking agent. Increased glutaraldehyde concentrations enhanced the mechanical properties of the scaffolds, bringing them closer to those of cancellous bone. Rat bone marrow mesenchymal stromal cells maintained their viability on these scaffolds compared to standard cell culture plates. In addition, these cells showed differentiation into bone lineage as evaluated from alkaline phosphatase activity up to 21 days and Alizarin red staining of the cells over 28 days. Eventually, scaffolds were implanted in a cranial defect in a rat animal model with a 5 mm diameter. Bone regeneration was studied over 90 days. Analysis of histological sections of the injury and computer tomography images revealed that nanocomposite scaffolds cross-linked with 1% w/v glutaraldehyde provide the maximum bone regeneration after 90 days. Collectively, our data show that nanocomposite scaffolds developed here provide effective regeneration for extensive bone defects in vivo .