Continental rifts are zones of lithospheric stretching and heating, but fundamental questions remain regarding the localization of rifting and magmatism during early-stage rifting. Few observations inform the distribution of magma intrusions in weakly-extended lithosphere. Controversy exists regarding the continuation of crustal shear zones in the mantle, and whether these sutures are weak zones that localize strain and magmatism during early-stage rifting. We use a new 3D lithospheric-scale resistivity models and existing seismic imaging to evaluate the roles of (1) magmatic modification and (2) pre-rift structural and compositional heterogeneity on rift localization of the Miocene-Recent Malawi rift, Africa. The bulk conductivity of these electric anomalies enables imaging of melt storage zones and provide constraints on physical properties of Proterozoic lithosphere. The 25-0 Ma Rungwe Volcanic Province (RVP) is underlain by low resistivity zone interpreted as magma storage in the crust (≤ 30 Ω⋅m at 8-20 km depth) and mantle-lithosphere (≤ 5 Ω⋅m at 30-70 km depth), with melt fraction estimates of 2-9 % and 7-17 %, respectively. Both inside and outside the Malawi rift, resistive Proterozoic orogenic terranes (3,000-10,000 Ω·m at 30-100 km depth) indicate dehydrated mantle-lithosphere and are bounded by linear conductive belts at lower-crust and upper-mantle depths (≤ 30 Ω·m at 25-50 km depth). The latter may reflect graphite within Proterozoic suture zones. Only short segments of Malawi rift border faults coincide with the interpreted as deep suture zones, and border faults cross cut these ancient structures.