The structure of igneous plumbing systems in circum-South Atlantic, intra-continental rift basins (e.g. the West and Central African Rift Systems) remains enigmatic owing to poor subsurface data coverage and quality. How magmatism in these basins related to the opening of the South Atlantic is thus poorly understood. We integrate 2D and 3D seismic reflection data (c. 27 600 km2), data from 23 boreholes, and field observations from the Bornu Basin and Upper Benue Trough, onshore NE Nigeria, to examine the timing and development of igneous bodies possibly related to opening of the South Atlantic. We identify numerous sills, which typically have saucer-shaped and en echelon morphologies, and extrusive volcanic cones. The igneous rocks are alkali basalts and dolerites. Seismic-stratigraphic relationships indicate that emplacement occurred in the Early Cretaceous (Albian to Cenomanian; c. 120 Ma), Late Cretaceous (Santonian to early Campanian; c. 83 Ma) and Cenozoic (Miocene; c. 22 Ma). Magmatism was broadly coeval with major plate boundary interactions, characterized by major azimuthal changes in fracture zones in the developing South Atlantic Ocean. The broad temporal correlation between intra-continental rift basin magmatism and plate boundary interactions suggests that periods of magma emplacement may have, in some way, been instigated by stress dissipation into intra-continental rift basins.