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The present-day distribution of Bantu languages is commonly thought to reflect the early stages of the Bantu Expansion, the greatest migration event in African prehistory. Using 1149 radiocarbon dates linked to 115 pottery styles recovered from 726 sites throughout the Congo rainforest and adjacent areas, we show that this is not the case. Two periods of more intense human activity, each consisting of an expansion phase with widespread pottery styles and a regionalization phase with many more local pottery styles, are separated by a widespread population collapse between 400 and 600 CE followed by major resettlement centuries later. Coinciding with wetter climatic conditions, the collapse was possibly promoted by a prolonged epidemic. Comparison of our data with genetic and linguistic evidence further supports a spread-over-spread model for the dispersal of Bantu speakers and their languages.