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SUMMARY Here, we investigate how continental rifts initiate and propagate across cratons by exploring the crustal structure of northwestern tip of the East African Rift System (EARS), hosting the volcanic-rich Edward-George and non-volcanic Albertine-Rhino rifts, and their termination at the Precambrian Aswa Shear Zone. We conducted a derivative analysis of magnetic data, utilized power spectral analyses and implemented a 2-D forward modelling of gravity data constrained by the seismic results obtained from the region. A magnetic derivative map indicates that the border faults of the Albertine Rift, at regional-scale, trend parallel to the Mesoproterozoic Madi-Igisi fold belt (MIFB) structures, representing the suture zone between two Archean microcratons. Our results show a pronounced thinned crust (∼24–30 km) beneath the southern segments of the rift zone, particularly the Edward-George rift, the Rwenzori Mountains and the southern Albertine graben, consistent with previous seismic studies. In general, we observe that: (1) the rift system follows the boundary between a broadly thinner crust (21–41 km) to the southeast in Uganda, and thick crust (34–41 km) to the northwest in Congo, and (2) within the rifts, the crustal thickness along the axes exhibits a strong gradient that attenuates northwards beneath the Albertine-Rhino graben. We supplement the geophysical results with field observations of an exhumed Permian ‘Karoo’ rift (Entebbe Graben) in central Uganda, indicating the possible source of inherited thinner crust to the southeast of the Albertine-Rhino Rift. We propose that the northwestern tip of the EARS exploited a cratonic crustal thickness-gradient, assisted by structural inheritance from crustal metamorphic fabrics, and potentially, thermomechanical weakening of the deeper crust by partial melts beneath some of the rift segments.