The poor structural stability of collagen (COL) upon hydration poses a significant challenge in tissue engineering (TE). To overcome this limitation, the incorporation of hydrophobic polymers such as poly(3-hydroxybutyrate) (PHB), and nanomaterials such as carbon nanotubes (CNTs) has been explored. In this study, we investigated the physical, chemical, and biological characteristics of COL-based scaffolds modified with PHB and CNTs for bone tissue engineering (BTE) applications. The tensile strength analysis revealed a substantial improvement in the ultimate tensile strength with the addition of 10 % PHB and 4 % CNTs. Scanning electron microscopy (SEM) images depicted a denser and more compact structure resulting from the presence of PHB and CNTs, enhancing the scaffold's mechanical properties. Fourier-transform infrared spectroscopy (FTIR) confirmed the successful incorporation of PHB and CNTs into the composite scaffold, maintaining the chemical integrity of COL. Stereological studies also conducted in a rat model with induced critical-sized bone defects in the mandibular bone further emphasize the substantial increase in bone formation and reduction in defect volume achieved by the scaffold loaded with stem cells. These findings underscore the promising approach to enhance bone healing, using COL-based scaffolds loaded with stem cells, and the favorable results obtained in this study can contribute to the advancement of BTE strategies.