The Ethiopian-Yemen plateaus have been affected by plume-related magmatism for at least 40 My, yet the nature and distribution of intrusive magmas and their relation to subsequent East Africa rifting remain poorly characterized. This paper presents a 3D shear (S) - wave velocity structure of the crust and uppermost mantle beneath the northern sectors of the East African rift and the dynamically-supported Ethiopian Plateau. We apply a Bayesian inversion of group and phase velocity dispersion curves for periods 5–40 s extracted from the ambient noise tomography of data from over 125 broadband seismic stations, and we identify seismic discontinuities using autocorrelation of P-wave coda. The resulting crustal structure affecting much of the Main Ethiopian Rift (MER) indicates a pronounced low S-wave velocity lower crust (∼3.6 km/s) that becomes thinner towards the northeast rising to almost the same depth level (∼20 km) as the base crust beneath the Afar triple junction zone. We also find high velocity features in the crust and uppermost mantle beneath the Afar rift axes, the current locus of strain and volcanism, that may indicate voluminous new basaltic crust. Our Moho-depth map indicates that the entire Afar Depression is underlain by crust thinner than 25 km, whereas the MER and central Ethiopian plateau are underlain by low S-wave velocity crust thicker than 35 km. These patterns suggest active underplating beneath the largely unfaulted plateau, in contrast to the efficient magmatic feeder system supplying a narrow zone of incipient seafloor spreading in the Afar depression. Within the uppermost mantle we report evidence of a localized asthenospheric upwelling beneath the western part of the plateau southeast of Lake Tana, overlying a cooled magma body within the upper crust. A broader low-velocity uppermost mantle underlies the crust beneath the Western Plateau. These observations attest to active mantle upwelling, heating, and melt intrusion at relatively different length scales beneath the plateau in agreement with the ongoing active strains reported away from the rift zones. At 45–60 km depth beneath the rift and its shoulders, we observe a fast lid (4.2–4.4 km/s). Beneath the plateau, upper mantle velocity highs that are at least 5 km below the Moho are observed. These areas have most likely experienced prolonged magma extraction and may mark highly depleted areas.