The geological evolution of northwestern Africa and its continental margins is investigated in the light of nine Meso-Cenozoic paleogeological maps, which integrate original minimal extent of sedimentary deposits beyond their present-day erosional limits. Mapping is based on a compilation of published original data on the stratigraphy and depositional environments of sediments, structures, magmatism, and low-temperature thermochonology, as well as on the interpretation of industrial seismic and borehole data. We show that rifting of the equatorial domain propagated eastward from the Central Atlantic between the Valanginian (ca. 140 Ma) and the Aptian (ca. 112 Ma) as an en echelon strike-slip and rift system connected to an inland rift network. This network defines a six-microplate synrift kinematic model for the African continental domain. We document persistent, long-wavelength eroding marginal upwarps that supplied clastic sediments to the offshore margin basins and a large intracratonic basin. The latter acted as a transient sediment reservoir because the products of its erosion were transferred both to the Tethys (to the north) and the Atlantic Ocean. This paired marginal upwarp-intra cratonic basin source-to-sink system was perturbed by the growth of the late Paleogene Hoggar hotspot swell that fragmented the intracratonic basins into five residual depocenters. By linking the evolution of the continental margins to that of their African hinterland, this study bears important implications for the interplay of long-wavelength deformation and sediment transfers over paired shield-continental margin systems.