Ceramic and metallic nanoparticles can improve the mechanical and biological properties of polymeric scaffolds for bone tissue engineering (BTE). In this work, nanohydroxyapatite (nHAp) and nano-copper-zinc alloy (nCuZn) were added to a chitosan/gelatin (Ch/G) scaffold in order to investigate the effects on morphological, physical, and biocompatibility properties. Scaffolds were fabricated by a freeze-drying technique using different pre-freezing temperatures. Microstructure and morphology were studied by scanning electron microscopy (SEM), glass transition (Tg) was studied using differential scanning calorimetry (DSC), cell growth was estimated by MTT assay, and biocompatibility was examined in vitro and in vivo by histochemistry analyses. Scaffolds and nanocomposite scaffolds presented interconnected pores, high porosity, and pore size appropriate for BTE. Tg of Ch/G scaffolds was diminished by nanoparticle inclusion. Mouse embryonic fibroblasts (MEFs) cells loaded in the Ch/G/nHAp/nCuZn nanocomposite scaffold showed suitable behavior, based on cell adhesion, cell growth, alkaline phosphatase (ALP) activity as a marker of osteogenic differentiation, and histological in vitro cross sections. In vivo subcutaneous implant showed granulation tissue formation and new tissue infiltration into the scaffold. The favorable microstructure, coupled with the ability to integrate nanoparticles into the scaffold by freeze-drying technique and the biocompatibility, indicates the potential of this new material for applications in BTE.