The causes of magmatism at magmatic rifted margins and large igneous provinces (LIPs) are uncertain because the condition of the mantle that underlay them during formation can no longer be directly observed. Therefore, whether the mantle was characterized by elevated potential temperatures (TP), small-scale convection, or anomalously fertile composition is debated. East Africa is an ideal area in which to address this problem because it contains both the young African-Arabian LIP and the tectonically and magmatically active East African Rift system. Here we present mantle TP estimates for 53 primitive magmas from throughout the region to reveal that thermal anomalies currently peak in Djibouti (140 °C above ambient upper mantle). Slightly warmer conditions accompanied the Oligocene African-Arabian LIP, when the TP anomaly was 170 °C. These values are toward the low end of the global temperature range of LIPs, despite the markedly slow seismic velocity mantle that underlies the region. Mantle seismic velocity anomalies in East Africa cannot, therefore, as is often assumed, be attributed simply to elevated mantle temperatures. We conclude that CO2-assisted melt production in the African superplume contributes to the markedly slow seismic velocities below East Africa.