The causes for the formation of large igneous provinces and hotspot trails are still a matter of considerable dispute. Seismic tomography and other studies suggest that hot mantle material rising from the core-mantle boundary (CMB) might play a significant role in the formation of such hotspot trails. An important area to verify this concept is the South Atlantic region, with hotspot trails that spatially coincide with one of the largest low-velocity regions at the CMB, the African large low shear-wave velocity province. The Walvis Ridge started to form during the separation of the South American and African continents at ca. 130 Ma as a consequence of Gondwana breakup. Here, we present the first deep-seismic sounding images of the crustal structure from the landfall area of the Walvis Ridge at the Namibian coast to constrain processes of plume-lithosphere interaction and the formation of continental flood basalts (Paraná and Etendeka continental flood basalts) and associated intrusive rocks. Our study identified a narrow region (<100 km) of high-seismic-velocity anomalies in the middle and lower crust, which we interpret as a massive mafic intrusion into the northern Namibian continental crust. Seismic crustal reflection imaging shows a flat Moho as well as reflectors connecting the high-velocity body with shallow crustal structures that we speculate to mark potential feeder channels of the Etendeka continental flood basalt. We suggest that the observed massive but localized mafic intrusion into the lower crust results from similar-sized variations in the lithosphere (i.e., lithosphere thickness or preexisting structures).