Soil organic C (SOC) stock assessments at the regional scale under climate change scenarios are of paramount importance in implementing soil management practices to mitigate climate change. In this study, we estimated the changes in SOC sequestration under climate change conditions in agricultural land in Spain using the RothC model at the regional level. Four Intergovernmental Panel on Climate Change (IPCC) climate change scenarios (CGCM2‐A2, CGCM2‐B2, ECHAM4‐A2, and ECHAM4‐B2) were used to simulate SOC changes during the 2010 to 2100 period across a total surface area of 2.33 × 104 km2. Although RothC predicted a general increase in SOC stocks by 2100 under all climate change scenarios, these SOC sequestration rates were smaller than those under baseline conditions. Moreover, this SOC response differed among climate change scenarios, and in some situations, some losses of SOC occurred. The greatest losses of C stocks were found mainly in the ECHAM4 (highest temperature rise and precipitation drop) scenarios and for rainfed and certain woody crops (lower C inputs). Under climate change conditions, management practices including no‐tillage for rainfed crops and vegetation cover for woody crops were predicted to double and quadruple C sequestration rates, reaching values of 0.47 and 0.35 Mg C ha−1 yr−1, respectively.Core Ideas The model predicted a general increase in SOC stocks by 2100 in all climate scenarios. Irrigated crops showed the largest SOC stocks. Carbon inputs were the most important driver for SOC stocks. No‐tillage and cover crops have at least doubled SOC sequestration rates.