Hydroxyapatite is widely used as a biomaterial filler to promote maxillofacial bone regeneration. Bacterial infections pose a common challenge to maxillofacial bone tissue regeneration; thus, incorporating antibacterial properties into hydroxyapatite-based scaffolds is essential. This study aimed to develop composite scaffolds for maxillofacial reconstruction by incorporating silver and iron nanoparticles into hydroxyapatite-polymer composites. A thermally induced phase separation method was employed to fabricate scaffolds with hydroxyapatite, collagen, and chitosan. Various characterization techniques, including porosity and density measurements, swelling ability analysis, biodegradability, FTIR, XRD, and SEM analysis, were utilized. The incorporation of silver and iron nanoparticles enhanced antibacterial properties and promoted bone growth. The scaffolds demonstrated efficacy against bacteria in antimicrobial assays. Cytotoxicity and blood biocompatibility analysis confirmed their compatibility with cells, and in vivo studies in a rabbit mandibular defect model demonstrated successful bone restoration. These findings may have significant implications for craniofacial tissue regeneration, particularly in non-load-bearing bone defects.