The ancient cores of continents (cratons) are underlain by mantle keels—volumes of melt-depleted, mechanically resistant, buoyant and diamondiferous mantle up to 350 kilometres thick, which have remained isolated from the hotter and denser convecting mantle for more than two billion years. Mantle keels formed only in the Early Earth (approximately 1.5 to 3.5 billion years ago in the Precambrian eon); they have no modern analogues1–4. Many keels show layering in terms of degree of melt depletion5–7. The origin of such layered lithosphere remains unknown and may be indicative of a global tectonics mode (plate rather than plume tectonics) operating in the Early Earth. Here we investigate the possible origin of mantle keels using models of oceanic subduction followed by arc-continent collision at increased mantle temperatures (150–250 degrees Celsius higher than the present-day values). We demonstrate that after Archaean plate tectonics began, the hot, ductile, positively buoyant, melt-depleted sublithospheric mantle layer located under subducting oceanic plates was unable to subduct together with the slab. The moving slab left behind craton-scale emplacements of viscous protokeel beneath adjacent continental domains. Estimates of the thickness of this sublithospheric depleted mantle show that this mechanism was efficient at the time of the major statistical maxima of cratonic lithosphere ages. Subsequent conductive cooling of these protokeels would produce mantle keels with their low modern temperatures, which are suitable for diamond formation. Precambrian subduction of oceanic plates with highly depleted mantle is thus a prerequisite for the formation of thick layered lithosphere under the continents, which permitted their longevity and survival in subsequent plate tectonic processes.