Biphasic calcium phosphate (BCP) nanoparticles were loaded with porous gelatin-pectin (GE-P) scaffolds. The biodegradable gelatin-pectin-BCP scaffolds were produced as miscible mixtures with well-defined interconnected pores to facilitate osteoconductivity and enhance bone formation. It was observed that the compressive strength increased with the loading of BCP nanoparticles. From in vitro results, cell adhesion, viability, and proliferation were found in the GE-P-10 scaffolds in comparison with those without BCP, resulting in high alkaline phosphate (ALP), and osteopontin (OPN) expression at 21 days. Micro-computed tomography data, hematoxylin and eosin staining, and immunohistochemistry (OPN, OCN, COL I, and COL II) confirmed rapid new bone formation in rabbit models. Our results provide a novel and simple method to provide an adequate scaffold, and thus GE-P-BCP porous scaffolds may be appropriate candidates for bone tissue engineering.