Continental break-up is controlled by several parameters and processes (rheology, inherited structures, magmatism, etc). Their impact, chronology and interactions are still poorly known and debated, particularly when rifting interacts with cratons. In order to better understand the rifting initiation in a cratonic lithosphere, we analysed 22 magnetotelluric (MT) soundings collected along two East-West profiles in two different rift segments of the North Tanzanian Divergence. The North Tanzanian Divergence, where the East African Rift is at its earliest stage, is a remarkable example of the transition between magmatic to amagmatic rifting with two clearly identified segments. Only separated by a hundred kilometers, these segments, Natron (North) and Manyara (South), display contrasted morphological (wide versus narrow), volcanic (many versus a few edifices) and seismic (shallow versus deep activity) signatures. Magnetotelluric profiles across the two segments were inverted with a three-dimensional approach and supplied the resistive structure of the upper lithosphere (down to about 70 km). The Natron segment has a rather conductive lithosphere containing several resistive features (Proterozoic Belt), whereas the Manyara segment displays highly resistive blocks probably of cratonic nature encompassing a conductive structure under the axial valley. The joint interpretation of these models with recent local and regional seismological studies highlights totally different structures and processes involved in the two segments of the North Tanzanian Divergence. We identified contrasted CO2 content, magma upwelling or trapping, in depth regarding the Manyara or the Natron branch and the influence of inherited cratonic structures in the rifting dynamics.