Currently, root canal therapy is the only clinical treatment available to treat damaged or necrotic dental pulp tissue arising from caries. This treatment results in the loss of tooth vitality. Somatic dental stem cell-based tissue engineering approaches can alleviate this problem by preserving tooth vitality. Dental stem cells are multipotent and under appropriate conditions could be used for dental pulp tissue engineering. Successful use of these cells in pulp repair requires a combination of growth factors and appropriate scaffolds to induce cell differentiation. In this study, we demonstrate the odontogenic differentiation of human dental pulp stem cells (DPSCs) and the human periodontal ligament stem cells when cultured on a decellularized 3D extracellular matrix (ECM) scaffold without the need for exogenous addition of growth factors. Subcutaneous implantation of the ECM scaffolds containing DPSCs showed the formation of dental pulp-like tissue with cells expressing dentin sialoprotein (DSP) and dentin phosphophoryn (DPP). Additionally, we also show that the ECM scaffold can be exploited as a tool to study the extracellular function of multifunctional proteins. These promising results demonstrate the feasibility of developing these biomimetic scaffolds for treatment of dental caries.