Ellagic acid (EA) is a potent antioxidant that reduces oxidative stress and promotes differentiation. By lowering the harmful levels of reactive oxygen species (ROS), EA fosters an environment conducive to the osteoblastic differentiation (OB) of stem cells. In addition, it promotes autophagy and mitophagy, which are vital for promoting differentiation. Effective autophagic activity recycles damaged organelles and proteins, meeting the energy required during differentiation and shielding from apoptosis. However, molecular mechanisms underlying the osteogenic differentiation of mesenchymal stem cells remain inadequately explored. Therefore, the current study aims to define the regulatory role of EA during the OB of dental pulp-derived stem cells (DPSC) and to study how autophagy and mitophagy are being modulated during this differentiation process. Herein, we showed that the expression level of osteoblast-specific markers, autophagy, and mitophagy-associated markers was significantly elevated during EA-mediated OB differentiation of DPSC. Moreover, we found that the EA induced the osteoblastic-specific markers through canonical BMP2 pathway molecules, reduced ROS in both basal and activated states, and induced autophagy and mitophagy molecules along with enhanced mitochondrial functions. Cell cycle analysis revealed that the G1 phase was arrested via phosphorylation of γ-H2AX, ATM, and CHK2 proteins. Furthermore, in silico analysis revealed that EA strongly binds with osteonectin, a crucial noncollagen protein involved in bone remodeling, and confirmed by Western blot analysis. These results support that EA could be a promising natural compound for bone repair and regeneration applications.