In bone tissue engineering, an ideal scaffold is required to have favorable physical, chemical (or physicochemical), and biological (or biochemical) properties to promote osteogenesis. Although silk fibroin (SF) and/or soy protein isolate (SPI) scaffolds have been widely used as an alternative to autologous and heterologous bone grafts, the poor mechanical property and insufficient osteoinductive capability has become an obstacle for their in vivo applications. Herein, β-tricalcium phosphate (β-TCP) and graphene oxide (GO) nanoparticles are incorporated into SF/SPI scaffolds simultaneously or individually. Physical and chemical properties of these composite scaffolds are evaluated using field emission scanning electron microscope (FESEM), X-ray diffraction (XRD) and attenuated total reflectance Fourier transformed infrared spectroscopy (ATR-FTIR). Biocompatibility and osteogenesis of the composite scaffolds are evaluated using bone marrow mesenchymal stem cells (BMSCs). All the composite scaffolds have a complex porous structure with proper pore sizes and porosities. Physicochemical properties of the scaffolds can be significantly increased through the incorporation of β-TCP and GO nanoparticles. Alkaline phosphatase activity (ALP) and osteogenesis-related gene expression of the BMSCs are significantly enhanced in the presence of β-TCP and GO nanoparticles. Especially, β-TCP and GO nanoparticles have a synergistic effect on promoting osteogenesis. These results suggest that the β-TCP and GO enhanced SF/SPI scaffolds are promising candidates for bone tissue regeneration.