Sequestering atmospheric carbon in soils is considered a key climate change mitigation strategy and including cover crops into cropping systems is commonly promoted as a management change that can increase soil organic carbon (SOC). Projecting SOC changes under climate change when cover crops are integrated into a cropping system is important because climate is a key driver of SOC dynamics and projected changes in climate are uncertain. Further, projecting SOC changes can provide landholders with information on the risk associated with the use of cover crops to generate carbon credits considering the inherent uncertainty in SOC changes under a changing climate. The Agricultural Production SIMulator was used to simulate SOC and yields of a typical crop rotation, with and without a cow pea cover crop, at 204 sites in the Riverina region of Southern Australia. Sowing cover crops reduced crop yields and increased SOC relative to the crop rotation without cover crops. GHG emissions associated with indirect land use change due to reduced crop yields and N2O emissions from the cover crop meant that sowing cover crops was unlikely to provide climate change mitigation. The number of carbon credits generated by participating in the soil carbon method of the Australian government’s emissions reduction program varied greatly across the region with some sites not generating any credits. The implications of these results are discussed with respect to climate change mitigation and the risk of entering a SOC trading program when costs of compliance are high and the ability to generate carbon credits is uncertain.