In this study, we prepared an electrospun nanofiber membrane from soya protein isolate (SPI) and polyethylene oxide (PEO) loaded with rat bone marrow-derived mesenchymal stem cells (rBMSC), as a cell-scaffold approach to enhance bone regeneration. Different ratios of SPI:PEO (7:0, 7:1, 7:3, 7:5, and 0:7) was investigated to obtain uniform nanofibers, and crosslinked with EDC/NHS to stabilize the membranes. SPI/PEO membrane (7:3) was found to create more uniform and stable nanofibers at a flow rate of 9 µL/min, spun in a cylindrical collector rotating at 350 r/min, 23 kV DC voltage, and needle tip to collector distance of 13 cm. The loaded rBMSC were pre-differentiated to ensure commitment towards osteoblastic lineage. The SPI/PEO electrospun nanofiber membranes were successful in allowing for cell attachment and growth of the rBMSC and was further investigated in vivo using a rat skull defect model. New bone formation was observed for the optimized SPI/PEO electrospun nanofiber membrane (7:3) with and without rBMSC, but with faster new bone formation for SPI/PEO electrospun nanofiber membrane loaded with rBMSC as compared to SPI/PEO electrospun nanofiber membrane only and control (defect only).