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Abstract The contribution of mantle upwellings of varying spatial extent to Cenozoic magmatism across Africa is debated because geochemical and seismological tools used to interrogate them are primarily sensitive to either composition or temperature. Thermochemical conditions control the depth at which mantle materials undergo phase changes, which cause seismic discontinuities. Mapping seismic discontinuities across the mantle transition zone (MTZ) and below provides insight into the variable thermochemical nature of upwellings. We present observations of seismic discontinuities beneath Africa obtained from a compilation of P‐to‐s receiver functions (RFs; using Pds, PPds, and PKPds phases), recorded at seismograph networks across Africa between 1990–2019. We exploit a recent high‐resolution African continental P‐wavespeed model to migrate our RFs to depth in a common conversion point stack. Cenozoic magmatism along the East African Rift is largely underlain by a thin MTZ implying a contribution to rift magmatism from sources at or below MTZ depths. The Ethiopian rift is underlain by a depressed d410 and uplifted d660 indicating a moderate positive thermal anomaly at MTZ depths (∼100–150 K). The southern East African Rift displays a greater d410 depression and a regional d660 depression, suggesting a stronger thermochemical anomaly at MTZ depths. Here, seismic conversions at ∼1,025 km depth are collocated with slow wavespeeds within the African Superplume, corroborating evidence for a compositional anomaly. We suggest that the contribution of a purely thermal plume directly below Ethiopia augments conditions for mantle melting and rifting. Distinct upwellings may also affect the MTZ below Cenozoic magmatism in Cameroon and Madagascar.