Peri-implantitis is an inflammatory disease that results in bone destruction around dental implants. A preclinical study using beagle models is frequently performed prior to clinical application in dentistry. Previously, we proposed an immediate peri-implantitis experimental model with a shorter experimental duration and less expense than the conventional experimental model. However, the differences in the regenerative outcomes between the immediate and conventional models were not fully revealed. In this study, we aimed to compare the regenerative outcomes between both models when ex vivo BMP2 gene therapy using autologous periodontal ligament stem cells (B2/PDLSCs) was applied to peri-implantitis defects. The results showed that the defect depths were significantly different between both models. New bone formation occurred in both models, but there were significant differences between the models. More than 70% of the defects were filled with newly formed bone in the conventional model, whereas 30-40% of the defects were filled in the immediate model. However, after adjustment for the differences in the defect depths between the models, the statistically significant differences in the regenerative outcomes between the models were lost. In conclusion, the inferior regenerative outcome of an immediate peri-implantitis model at B2/PDLSCs transplantation resulted from the defect depths, not the model itself.