Here we investigate the thermal structure of the mantle beneath the eastern Branch of the East African Rift system in Kenya and Tanzania. We focus on the structure of the mantle transition zone, as delineated by stacking of receiver functions. The top of the transition zone (the 410 km discontinuity) displays distinctive topography, and is systematically depressed beneath the rift in Kenya and northern Tanzania and adjacent volcanic fields. This depression is indicative of a localized ∼350 °C thermal anomaly. In contrast, the bottom of the transition zone (the 660 km discontinuity) is everywhere depressed. This region-wide depression is best explained as a Ps conversion from the majorite–perovskite transition of anomalously warm mantle. We interpret this structure of the transition zone as resulting from the ponding of a mantle plume (possibly the deep-mantle African Superplume) at the base of the transition zone, which then drives localized thermal upwellings that disrupt the top of the transition zone and extend to shallow mantle depths beneath the rift in Kenya and northern Tanzania.