A model of the thermal, compositional, density, and seismological structure of the lithospheric and sublithospheric mantle along a 500-km transect across the Namibian volcanic passive margin is presented. This margin juxtaposes old oceanic lithosphere and a Precambrian continental domain. The model combines within an internally consistent framework data from petrology, mineral physics, and geophysical observables. The calculated mantle temperature and density distributions down to a depth of 400 km are consistent with available xenolith-derived data, and fit simultaneously the observed free-air anomaly, geoid height, surface heat flow, and elevation. The model also explains the anomalously thick oceanic crust and the depletion of the lithospheric mantle in the ocean–continent transition and in the Proterozoic continental domain. Seismic velocities predicted by the present model are in good agreement with values obtained from wide angle reflection/refraction and tomography experiments. The thermal lithospheric thickness is ~ 100 km in the oceanic domain, increasing gradually to ~ 125 km across the ocean–continent transition and then more sharply to ~ 175 km in the continental domain. The density distribution in the mantle differs significantly from current purely thermal approaches where density is assumed to be only temperature-dependent. Non-negligible compositional density differences are encountered between the oceanic, transitional, and continental domains. Results show that non-thermal effects such as composition and phase changes cannot be neglected in models of the upper mantle.