2D seismic reflection data tied to biostratigraphical and log information from wells in the central and southeastern Alboran Sea have allowed us to constrain the spatial and temporal distribution of rifting and inversion. Normal faults, tilted basement blocks, and growth wedges reveal a thinned continental crust that formed in response to NW‐SE extension. To the east, a secondary SW‐NE trend of extension affects the transitional crust adjacent to the oceanic Algerian Basin. The maximum thickness of syn‐rift sediments is ~3.5 km, and the oldest recorded deposits are Serravallian. The WNW‐ESE Yusuf fault formed a buttress separating and accommodating variable extension between two different tectonic domains: the thinned continental crust of Alboran and the oceanic spreading of the Algerian Basin. Late Tortonian to present‐day NW‐SE Africa/Eurasia plate convergence drove shortening and reactivation of some of the earlier extensional structures as reverse and strike‐slip faults, forming complex, compartmentalised subbasins. Tectonic inversion coexisted with the formation of new faults and folds. Inversion was partial along the Habibas Basin and Al‐Idrisi fault, but complete along the Alboran Ridge, where some SW‐NE trending faults were perpendicular to the recent NW‐SE plate convergence and were reactivated as thrusts. The WNW‐ESE Yusuf fault is oblique to the convergence vector, and therefore, reactivation is mainly expressed as transpressional deformation. Volcanic rocks intruded along the Alboran Ridge and Yusuf faults during the latest stages of extension formed rheological anisotropies that localised the later inversion.