Introduction: The global issue of tissue damage and organ failure has led to increased interest in bioactive ceramics like hydroxyapatite(HAp), beta-tricalcium phosphate(β-TCP), and biphasic calcium phosphate for bone repair and regeneration. These materials stimulate cell growth and differentiation and directly bond with living tissues. The use of biogenic waste materials in healthcare offers economic, environmental, and societal benefits. Aim: This study focused on creating 3D polymeric scaffolds composed of PCL/zein and loaded with calcium phosphate ceramic fillers. These included HAp, synthesized from pure chemicals, and biphasic HAp/β-TCP derived from biogenic cancellous bovine bone(CBB), targeting bone tissue engineering(BTE) applications. Methodology: Nano-HAp and HAp/β-TCP ceramic powders were prepared from CBB waste and pure chemical reagents. These were blended with PCL/Zein polymer scaffolds through solvent casting/particulate leaching. The scaffolds underwent evaluation for their pore structure, compressive strength, porosity, bioactivity, and biodegradation rate using scanning electron microscopy (SEM) and other techniques. Results: SEM analysis revealed scaffolds with highly interconnected pores, ranging from 279to305 µm. The composite scaffold with HAp from pure reagents exhibited the highest compressive strength. However, the mechanical strength of scaffolds containing ceramics from CBB was comparable to cancellous bone. There were negligible differences in weight loss among the groups after six months in phosphate-buffered saline (PBS). Bioactivity was confirmed in all groups, indicated by new apatite crystal formation on surfaces after 14 days in PBS. Conclusion: Nano calcium phosphates derived from CBB waste are cost-effective and suitable for developing biocompatible scaffolds for BTE, offering a promising solution for bone regeneration applications.