We report on an ancient-yet-extant indigenous soil management system in West Africa wherein targeted waste deposition transforms highly-weathered, nutrient- and carbon-poor tropical soils into enduringly fertile, carbon-rich black soils. These “African Dark Earths (AfDE)”, store 200-300% more organic carbon with 2-26 times greater pyrogenic carbon (PyC) that persists much longer in soil than other organic carbon, and therefore important for long-term soil fertility and carbon storage. Compared to strongly acidic (pH 4.3-5.3) adjacent soils (AS), AfDE exhibit higher pH (5.6-6.4) ideal for plant growth, 1.4-3.6 times higher plant nutrient retention and exchange capacity, and 1.3-2.2 and 5-270 times more plant-available nitrogen and phosphorus, respectively. Despite limited areas, AfDE make disproportionately high contributions (24%) to total farm household income. 14C radiocarbon ages of pyrogenic carbon (PyC) indicate recent development (115-692 years BP). AfDE are an appropriate “climate-smart” agricultural alternative to conventional agriculture to tackle the “trilemma of soil degradation and food security and climate change challenges” in resource-poor, highly food-insecure regions of the world.