Warm season perennial C4 grasses (WSGs), switchgrass (Panicum virgatum L.) and miscanthus species (Miscanthus spp.), have been reported to positively influence short-term (15–20 years) soil organic carbon (SOC). In this study, the DayCent model was used to predict changes in long-term SOC stocks under WSGs for moderate (Representative Concentration Pathway (RCP) 4.5) and high (RCP 8.5) warming climate change scenarios in southern Ontario, Canada, and to determine how long the enhanced SOC stock will last when WSGs are converted back to annual crop rotation. The model predicted that a consistent corn–corn–soybean–winter wheat (CCSW) rotation prevented SOC from depletion over the 21st century. Under WSGs, the model predicted high rates of SOC sequestration during the first 20–30 years which then tended to stabilize after 50–60 years. However, the rate of SOC sequestration over 90 years for RCP 4.5 was 0.26 and 0.94 Mg C ha⁻¹ yr⁻¹ for switchgrass and miscanthus, respectively. If 40-year stands of WSGs are converted back to CCSW, the model predicted SOC decline to the previous level in 40–50 years. DayCent predicted that under RCP 8.5 scenario in the second half of the 21st century and in the future, there will be a reduction in SOC stocks, especially under miscanthus stands.