To evaluate the effect of non-viral gene therapy on human dental pulp stem cells (DPSCs) in an in vitro and an ex vivo model. Nanoplexes comprising polyethyleneimine (PEI) and plasmid DNA (pDNA) encoding for fibroblast growth factor-2 (pFGF-2) and bone morphogenic protein-2 (pBMP-2) were cultured with DPSCs to evaluate cytotoxicity, protein expression, and mineralization activity. Collagen scaffolds loaded with these nanoplexes or mineral trioxide aggregate (MTA) were utilized in an ex vivo tooth culture model to assess pulp response, over a period of 14days. All nanoplex formulations were characterized for size and zeta potential by measuring dynamic light scattering and electrophoretic mobility, respectively. DPSCs treated with the nanoplexes showed increased cell proliferation and enhanced expression of BMP-2 and FGF-2 proteins. Collagen scaffolds containing PEI-pBMP-2 and/or pFGF-2 nanoplexes significantly increased cell proliferation, BMP-2 and FGF-2 expression, and mineralization when compared to MTA. Ex vivo histology showed a well-preserved pulp and healthy tissue in both the MTA and scaffold groups. Connective tissue in contact with the scaffold was dense and homogeneous, with some cells present in contact and within the scaffold. Transfection of DPSCs with pBMP-2/pFGF-2 nanoplexes resulted in increased expression of BMP-2 and FGF-2, enhanced proliferation, and mineralization properties compared to MTA. These findings were supported by the ex vivo observations. This biological approach in pulp capping brings new insights into the effective management of engineered pulp tissues, mainly those generated by the transplantation of DPSCs in empty root canals.