Seismic imaging beneath shallow (<5 km) Palaeogene basaltic volcanic successions on the Faroe–Shetland Margin is very challenging with conventional seismic methods. Consequently, the interpretational uncertainty that surrounds the sub-basalt structure of the region is a major source of exploration risk. This study uses gravity and magnetic data in conjunction with seismic data to map the sub-basalt structure of the Faroe–Shetland Basin and model the crustal architecture of this part of the Atlantic margin. Four crustal types are recognized using gravity data: oceanic, intruded transitional, stretched continental and normal continental crust. Map-based interpretation of the gravity and magnetic data helps redefine the basins, highs and faults in the region. The structural interpretation suggests that the boundary between normal and stretched continental crust is coincident with the long-lived left-lateral ‘West Shetland Shear Zone’, which partitioned strain during rifting of the margin. 2D/2.5D gravity and magnetic models are shown for two seismic profiles from the PGS FSB MegaSurveyPlus. The models suggest highly thinned crust, which was intruded by mafic magma beneath the Flett sub-basin, and an asymmetry to the rifting, which is consistent with a process of Wernicke simple shear.