The complex structure of the North-East Greenland margin is the consequence of two rifting events: the initial separation of Greenland and Scandinavia around 56 Ma, and the breaking off of the Jan Mayen microcontinent from Greenland around 33 Ma likely driven by the arrival of the Iceland Plume beneath the east coast of Greenland. The boundary between these two rifting events is the Jan Mayen Fracture Zone. While seismic lines north of this pronounced topographic structure document the presence of a high velocity lower crust, existing data south of the fracture zone show no indications that the lower crust consists of a large, high velocity body. This gap is closed by a 500 km long seismic transect, which starts in Kong Oscar Fjord and extends out beyond the Kolbeinsey Ridge. It provides a detailed view of the crustal structure just south of the Jan Mayen Fracture Zone. The transect includes parts of the Caledonian crust of Greenland, crosses the present-day shelf and the oceanic crust formed since the separation of the Jan Mayen microcontinent. The seismic refraction line shows a constant ~9 km thick oceanic crust between the extended continental margin and the mid-ocean ridge. Evidence for an only 3 km thick high-velocity lower crustal body is observed within the continent-ocean transition zone. While such high velocity crust is ubiquitous beneath the shelf to the north of the fracture zone, to the south it only occurs beneath Mesozoic basins that have been attributed to extensional collapse of the Caledonian orogeny. Inline with earlier interpretations of high velocities in the lower crust of extended continental margins, we suggest that Kong Oscar Fjord is underlain by the products of excess magma production that were focused along the Jan Mayen Fracture Zone during the breakup of the Jan Mayen microcontinent from Greenland.