In this study, we explore the origin of lower crustal seismicity and the factors controlling rift propagation using seismological data recorded within the youngest part of the East African Rift System, the North Tanzanian Divergence (NTD). Most earthquakes below Lake Manyara occur at depth ranging between 20 and 40 km and have a swarm-like distribution. Focal mechanisms of 26 events indicate a combination of strike-slip and normal faulting involving Archaean basement structures and forming a relay zone. The derived local stress regime is transtensive and the minimum principal stress is oriented N110°E. Crustal seismic tomography reveals low-velocity anomalies below the rifted basins in the NTD, interpreted as localized thermomechanical perturbations promoting fluid release and subsequent seismicity in the lower crust. SKS splitting analysis in the NTD indicates seismic anisotropy beneath 17 stations most likely due to aligned magma lenses and/or dikes beneath the rift and to the lithospheric fabrics. Our results favor a strain pattern intermediate between purely mechanical and purely magmatic. We suggest that melt products arising from a large asthenospheric thermal anomaly enhance lithospheric weakening and facilitate faulting and creeping on critically oriented inherited structures of the Precambrian lower crust. Although the crust is unlikely weakened at a point comparable to other parts of the East African Rift System, this deep-seated thermomechanical process is efficient enough to allow slow rift propagation within the eastern Tanzanian cratonic edge.