Existing scaffolds cannot adequately satisfy the simultaneous requirements for the regeneration of bone. The challenge remains of how to improve the integration of newly formed bone with the surrounding tissues. The purpose of this study was to investigate the effects of two silk fibroin scaffolds, a hexafluoro isopropanol-based silk fibroin (HFIP-F) and an aqueous-based silk fibroin (A-F), for their osteoinductive potentials in large critical size bone defects in vivo. β-tricalcium phosphate (β-TCP) was used as a positive control. After implantation into defects created in the knee joints of rabbits for 1 and 2 weeks, hematoxylin and eosin (H-E) and Azan staining revealed that the A-F scaffold as well as β-TCP had stronger osteoinductive ability than the HFIP-F scaffold. The A-F scaffold exhibited prominent areas of neo-tissue containing bone-like nodules. Furthermore, induced osteointegration was observed between native and neo-tissue within the osteo defects in the knee joints of rabbits. Immunohistochemical staining showed the highest expression of Runx2, BMP-2, BMP-7, Smad1/5/9 and Phospho-Smad in the A-F scaffold implants. Osteoinduction of the porous A-F scaffold might be influenced by the amount of BMP signaling present in the local microenvironment in the implants. This study opens a new avenue to use A-F silk fibroin scaffolds for the regeneration of bone defects.