We present a joint analysis of newly acquired gravity and teleseismic data in the North Tanzanian Divergence, where the lithospheric break-up is at its earliest stage. The impact of a mantle upwelling in more mature branches of the East African Rift has been extensively studied at a lithospheric scale. However, few studies have been completed that relate the deep-seated mantle anomaly detected in broad regional seismic tomography with the surface deformation observed in the thick Archaean Pan-African suture zone located in North Tanzania. Our joint inversion closes the gap between local and regional geophysical studies, providing velocity and density structures from the surface down to ca. 250  km depth with new details. Our results support the idea of a broad mantle upwelling rising up to the lithosphere and creating a thermal modification along its path. However, our study clearly presents an increasing amplitude of the associated anomaly both in velocity and density above 200 km depth, which cannot be solely explained by a temperature rise. We infer from our images the combined impact of melt (2–3 per cent), composition and hydration that accompany the modification of a thick heterogenous cratonic lithosphere are a response to the hot mantle rising. The detailed images we obtained in density and velocity assert that Archaean and Proterozoic units interact with the mantle upwelling to restrict the lithosphere modifications within the Magadi–Natron–Manyara rift arm. The composition and hydration variations associated with those units equilibrate the thermal erosion of the craton root and allow for its stability between 100 and 200  km depth. Above 80 km depth, the crustal part is strongly affected by intruding bodies (melt and gas) which produces large negative anomalies in both velocity and density beneath the main magmatic centres. In addition to the global impact of a superplume, the velocity and density anomaly pattern suggests a 3-D distribution of the crust and mantle lithospheric stretching, which is likely to be controlled by inherited fabrics and enhanced by lateral compositional and hydration variations at the Tanzanian craton-orogenic belt boundary.