We study the formation and evolution of the Jan Mayen microcontinent (JMMC) in the framework of conjugate margin evolution in the Norwegian–Greenland Sea. The JMMC structural map and crustal architecture have been constrained by seismic mapping and potential field modelling, supplemented by published seismic refraction transects. The sedimentary and basement geometries have been further studied together with their conjugate to refine our knowledge on the less explored microcontinent. Structurally, the JMMC main ridge is characterized by a platform and/or terrace architecture flanked by sag type basins, similar to those described on the mid-Norwegian conjugate margin, while its southern part is marked by windows exposing crustal and/or mantle material that was exhumed during higher degrees of extension. The eastern side of the JMMC broke up in a magma-rich fashion, while the western side is magma poor. The limited amount of magma involved in the JMMC formation suggests that changes in far field forces were the driving mechanism to initiate the isolation process and that a mantle plume had a lesser influence, but might have helped the final mid-ocean ridge establishment between the western Jan Mayen and Greenland margin.