Significance Our results identify the prime driver of climate variation in Africa’s low latitudes over the past 620 ky—the key time frame for the evolution of our species. Warming and cooling of the tropical Pacific Ocean paced by insolation changes modulated the tropical Walker circulation, driving opposing wet–dry states in eastern and western Africa. We show that the effects of glacial/interglacial cycles were not the predominant source of environmental change in most of the continent. Africa’s environmental patchwork driven by low-latitude climate processes should therefore be a critical component in conceptual models of human evolution and early demography over the past 620 ky.