The East African rift (EAR) system formed on the slow-moving African continent, which last experienced orogeny during the Pan-African (800-500 Ma). We synthesize geophysical constraints interpreted in light of geochemical and geological data to evaluate the role of magmatism in shaping Africa’s crust, and as a consequence, basin stratigraphy. In young magmatic rift zones (<3 My), melt and volatiles are migrating from the asthenosphere to gas-rich magma reservoirs at the Moho, altering crustal composition and rheology during rift initiation. Energetic lower crustal and upper mantle earthquakes in areas of magmatic CO2 emissions indicate that deep magma intrusion, grain size and thermal stresses, and volatile degassing assist in strain localization within cratonic lithosphere. Within the <7 My southern sector of the Eastern rift, the crust comprises ~20% new magmatic material intruded as sills in the lower crust (underplate), and as localized sills and dike intrusions at shallower depths. In the mature Main Ethiopian rift, intrusions comprise 30% of the crust below axial rift zones of dike intrusion-dominated extension. In the incipient rupture zones of the Afar rift, magma intrusions fed from crustal magma chambers beneath segment centers create new columns of mafic crust, as along slow-spreading ridges. Our comparisons suggest that transitional crust, including seaward-dipping sequences, is created as progressively-smaller screens of continental crust are heated and weakened by repeated episodes of magma intrusion and extrusion into subsiding basins immediately prior to seafloor spreading. Our synthesis of crustal studies beneath zones of active rifting and orogenesis in Africa show that magma and volatiles are migrating from the asthenosphere through the plates, capturing carbon beneath deep cratons that is guided upward by topography at the lithosphere-asthenosphere boundary. The CO2-rich magmas release volatiles that embrittle the upper mantle and lower crust, explaining the crustal-scale basin-bounding faults, and the maintenance of half-graben morphologies during early-stage rifting. As the mantle lithosphere thins by bottom-up heating and dynamic advection, crustal magmatic systems and consequently, magmatism, localize. Surface, internal and sub-surface loads during middle to late-stage rifting lead to the creation of seaward-dipping sequences prior to the onset of MORB-type magmatism.