Bone defects are common and persistent problems in clinical orthopedics and dentistry. The development of synthetic reconstruction materials is essential owing to the restricted access to natural bone grafts, disease transmission risks, surgical costs, donor-site morbidity, infections, and immune response-related complications. The present study was done to evaluate the histopathological, histomorphometrical, and radiological characteristics of composite foams containing hydroxyapatite/bioactive glass (HA/BG) and fluorapatite/bioactive glass (FA/BG) as cell scaffolds in rat tibia reconstruction. A total of 60 rats were divided into four equal groups, of which three groups were implanted with HA/BG, FA/BG, and CenoBone biomaterials, and the fourth group served as the implant-free controls. Five rats from each group were sacrificed at 15, 30, or 60 days after implantation, and radiological, histopathological, and histomorphometrical assessments were carried out. Based on the findings, no foreign body reaction was present in the rats. Additionally, bone-biomaterial contact occurred directly without the involvement of connective tissues. The number of osteoblasts was reduced in the implant groups, whereas the trabecular thickness and rate of new bone formation were increased in all groups, where the increase in the FA/BG group was the most prominent. The mean percentage difference in bone density between the implant site and the host bone was greater in the FA/BG group at all three time points of the study. Based on the results of the present study and the positive characteristics of these nanocomposite foams, they can be suitable options for implantation in damaged tissues in tissue engineering.