Mantle upwellings drive large-scale surface volcanism and facilitate continental breakup and ocean basin formation. However, the spatial characteristics and internal composition of these upwellings alongside how they are modified by plate tectonics are poorly resolved. Afar, East Africa, is a classic triple junction comprising three rifts at various stages of evolution thought to be underlain by a mantle upwelling or plume, allowing examination of the controls on the mantle upwelling. Here we present geochemical data from >130 samples of ‘young’ volcanoes spanning the rifts defining the triple junction to show that the underlying mantle comprises a single, asymmetric upwelling. Using statistical modelling to integrate our data with existing geochemical and geophysical constraints, we suggest that Afar is fed by a spatially and chemically heterogeneous upwelling, which controls the composition and relative abundance of melt in all three rift arms. We identify repetitive signatures in mantle compositions in rift regions, whose variability is a longer wavelength in faster-extending rift arms. This suggests more rapid channelized mantle flow occurs where rifting rates are higher and the plate is thinner, aiding flow of the upwelling towards the faster-spreading Red Sea Rift. Our findings demonstrate how the evolution of mantle upwellings is influenced by the dynamics of overriding plates.