Calcium carbonate (CaCO3 ) plays a crucial role in influencing the growth of osteoblast. This study was conducted to compare the performance of alginate/cockle shell powder nanobiocomposite (nCP) bone scaffold developed from naturally occurring CaCO3 with alginate/calcium carbonate (CC) bone scaffold developed using synthetic CaCO3. The study compares the performance of the scaffold in supporting the growth of osteoblast through in vitro evaluations as well as initial biocompatibility observations through in vivo methods. Both scaffolds were developed using the mixture of 40% alginate solution with either 60% of nano cockle shell powder or synthetic CaCO3 to obtain a three dimensional scaffold structure. In vitro evaluation on calcium release and ALP enzyme activity was conducted on both scaffolds seeded with osteoblast on day’s three, five and seven using commercial kits. In vivo observations using histological methods were further conducted by implanting osteoblast seeded scaffold subcutaneously at the dorsum of 8 albino mice for 21 days. Findings from in vitro studies showed a significant increase (p < 0.05) in the release of calcium and ALP enzyme activity in nCP scaffolds on day seven compared to days three and five of CC scaffold. Histological observations using H&E and von Kossa staining showed infiltration and proliferation of osteoblast on both scaffolds as well as early stage bone tissue formation. Formation of new blood vessels within the scaffolds was also observed in nCP scaffold. Both the developed scaffolds were noted to support osteoblast growth and new tissue formation with better potentials displayed by nCP scaffolds comparatively. This study shows that naturally occurring CaCO3 obtained from cockle shells in the form of nano powder has good potentials to be used as a biomaterial for bone tissue engineering applications.