Increasing the amount of soil organic carbon (SOC) has agronomic benefits and the potential to mitigate climate change. Previous regional predictions of SOC trends under climate change often ignore or do not explicitly consider the effect of crop adaptation (i.e., changing planting dates and varieties). We used the DayCent biogeochemical model to examine the effect of adaptation on SOC for corn and soybean production in the U.S. Corn Belt using climate data from three models. Without adaptation, yields of both corn and soybean tended to decrease and the decomposition of SOC tended to increase leading to a loss of SOC with climate change compared to a baseline scenario with no climate change. With adaptation, the model predicted a substantially higher crop yield. The increase in yields and associated carbon input to the SOC pool counteracted the increased decomposition in the adaptation scenarios, leading to similar SOC stocks under different climate change scenarios. Consequently, we found that crop management adaptation to changing climatic conditions strengthen agroecosystem resistance to SOC loss. However, there are differences spatially in SOC trends. The northern part of the region is likely to gain SOC while the southern part of the region is predicted to lose SOC.