This study reveals rapid and severe soil degradation following deforestation in the Eastern African Rift, with cropland soils on mafic parent material losing up to 69% of their soil organic carbon. At the same time, reactive metal phases were found to stabilize soil organic carbon in highly degraded mafic soils despite strongly reduced fertility indicators. These findings suggest that soil organic carbon content may not always reflect soil fertility in degraded tropical soils. These results provide important insights for sustainable land management and food security in tropical Africa.