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This research aimed to assess the effect of bone allograft combined with platelet-rich plasma (PRP), recombinant human bone morphogenetic protein-2 (rhBMP-2), and zoledronic acid (Zol) on bone formation. A total of 96 rabbits were used, and femoral bone defects (5 mm) were created. The rabbits were divided into four groups: (1) bone allograft with PRP (AG + PRP), (2) bone allograft with rhBMP-2 5 μg (AG + BMP-2), (3) bone allograft with Zol 5 μg (AG + Zol), and (4) bone allograft (AG). A histopathological examination was performed to evaluate bone defect healing after 14, 30, and 60 days. The new bone formation and neovascularization inside the bone allograft was significantly greater in the AG + PRP group compared to AG and AG + Zol groups after 14 and 30 days (p < 0.001). The use of bone allograft with rhBMP-2 induced higher bone formation compared to AG and AG + Zol groups on days 14 and 30 (p < 0.001), but excessive osteoclast activity was observed on day 60. The local co-administration of Zol with a heat-treated allograft inhibits allograft resorption as well as new bone formation at all periods. In conclusion, this study demonstrated that PRP and rhBMP-2, combined with a Marburg bone allograft, can significantly promote bone formation in the early stage of bone defect healing.