Spinal cord injury (SCI) can lead to significant bone loss below the level of the lesion increasing the risk of fracture and increased morbidity. Body-weight-supported treadmill training (BWSTT) and transplantation strategies using neurotrophins have been shown to improve motor function after SCI. While rehabilitation training including BWSTT has also been effective in reducing bone loss post-SCI, the effects of transplantation therapies in bone restoration are not fully understood. Furthermore, the effects of a combinational treatment strategy on bone post-SCI also remain unknown. The aim of this study was to determine the effect of a combination therapy including transplantation of scaffold-releasing neurotrophins and BWSTT on the forelimb and hindlimb bones of a T9-T10 contused SCI animals. Humerus and tibia bones were harvested for Micro-CT scanning and a three-point bending test from four animal groups, namely injury, BWSTT (injury with BWSTT), scaffold (injury with scaffold-releasing neurotrophins), and combinational (injury treated with scaffold-releasing neurotrophins and BWSTT). BWSTT and combinational groups reported higher biomechanical properties in the tibial bone (below injury level) and lower biomechanical properties in the humerus bone (above injury level) when compared to the injury and scaffold groups. Studied structural parameters, including the cortical thickness and bone volume/tissue volume (BV/TV) were also higher in the tibia and lower in the humerus bones of BWSTT and combinational groups when compared to the injury and scaffold groups. While no significant differences were observed, this study is the first to report the effects of a combinational treatment strategy on bone loss in contused SCI animals and can help guide future interventions.