Reconstruction of extensive bone defects due to age, trauma, or post-illness conditions remains challenging. Biomimetic scaffolds with osteogenic capabilities have been proposed as an alternative to the classical autograft and allograft implants. Three-dimensional scaffolds were obtained based on Ce-doped mesoporous bioactive glass (MBG) and Spongia agaricina (SA) as sacrificial templates functionalized with vitamin D₃. The study aimed to investigate the effect of vitamin D₃ functionalization on the optimal variant of a 3D scaffold doped with 3 mol% ceria, selected in our previous work based on its biological and physicochemical properties. Scanning electron microscopy (SEM) images of the non-functionalized/functionalized scaffolds revealed a porous structure with interconnected pores ranging from 100 to 350 μm. Fourier transform infrared spectroscopy (FTIR) and SEM analysis confirmed the surface functionalization. Cytotoxicity evaluation showed that all investigated scaffolds do not exhibit cytotoxicity and genotoxicity toward the Saos-2 osteosarcoma cell line. Moreover, the study demonstrated that functionalization with vitamin D₃ enhanced osteogenic activity in dental pulp stem cells (DPSCs) by increasing calcium deposition and osteocalcin secretion, as determined by Alizarin red stain and a colorimetric ELISA kit, as a result of its synergistic action with cerium ions. The results showed that the Ce-doped MBG scaffold functionalized with vitamin D₃ had the potential for applications in bone regeneration.