The ideal construction and tissue substitute with adjusted characteristics and functionalities for the regeneration of bone defects are still under investigation. Current approaches have focused on the use of various biocompatible materials that have been synthesized with carbon-based materials with physicochemical characteristics that contribute to the differentiation of specific stem cell lineages. This work reports on the potential of poly-ε-caprolactone (PCL) membranes loaded with β-glycerol phosphate (β-GP) functionalized multiwall carbon nanotubes (f-MWCNTs) to induce differentiation of human dental pulp stem cells (HDPSCs) into osteoblasts. The HDPSCs were seeded on unmodified PCL + f-MWCNTs and β-GP decorated PCL + f-MWCNTs membranes, and then, physicochemical, mechanically and biologically characterized. It was observed an increase in the mechanical properties of PCL by MWCNTs addition rendering a more hydrophilic membrane those containing β-GP. Live/Dead and MTT cytotoxicity tests showed a higher number of living cells in PCL + f-MWCNTs + β-GP membranes, whereas von Kossa showed calcium deposits. After Wistar rat implantation, new bone formation was found around the critical size calvaria defects indicating that these membranes have the ability to enhance the osteodifferentiation of HDPSCs by increasing mineralization.