Southern Africa is facing a unique combination of high rates of current food insecurity and projected declines in agro-climatic conditions due to climate change. Here we show using multiple satellite measures that, outside of South Africa, countries in the region have not experienced significant gains in cropland productivity in the past 20 years. This view contrasts with the rosier picture painted by official crop yield records. Satellite productivity measures show clear interannual responses to temperature and rainfall, yet we find that recent climate trends do not explain the productivity stagnation. Instead, much of the region has benefitted from increased rainfall and less warming than projected by most climate model simulations. Our results suggest that the region missed an opportunity to raise productivity in the face of benign climate trends, and there is a clear and urgent need to change course before climate impacts accelerate.