How cratons, the ancient cores of continents, evolved since their formation over 2.5 Ga ago is debated. Seismic tomography can map the thick lithosphere of cratons, but its resolution is low in sparsely sampled continents. Here we show, using waveform tomography with a large, newly available dataset, that cratonic lithosphere beneath Africa is more complex and fragmented than seen previously. Most known diamondiferous kimberlites, indicative of thick lithosphere at the time of eruption, are where the lithosphere is thin today, implying surprisingly widespread lithospheric erosion over the last 200 Ma. Large igneous provinces, attributed to deep-mantle plumes, were emplaced near all lithosphere-loss locations, concurrently with or preceding the loss. This suggests that the cratonic roots foundered once modified by mantle plumes. Our results imply that the total volume of cratonic lithosphere has decreased since its Archean formation, with the fate of each craton depending on its movements relative to plumes.