Many savannas in West Africa have been converted to croplands and are among the world’s regions most vulnerable to climate change due to deteriorating soil quality. We focused on the savanna-derived cropland in northern Ghana to simulate its sensitivity to projected climate change and nitrogen fertilization scenarios. Here we show that progressive warming–drying stress over the twenty-first century will enhance soil carbon emissions from all kinds of lands of which the natural ecosystems will be more vulnerable to variation in climate variables, particularly in annual precipitation. The carbon emissions from all croplands, however, could be mitigated by applying nitrogen fertilizer at 30–60 kg N ha − 1 year − 1. The uncertainties of soil organic carbon budgets and crop yields depend mainly on the nitrogen fertilization rate during the first 40 years and then are dominated by climate drying stress. The replenishment of soil nutrients, especially of nitrogen through fertilization, could be one of the priority options for policy makers and farm managers as they evaluate mitigation and adaptation strategies of cropping systems and management practices to sustain agriculture and ensure food security under a changing climate.