Near-orthogonal ultra-slow (13.3 mm yr− 1 to 6.5 mm yr− 1) sea floor spreading in the absence of large transform faults make the Arctic Gakkel Ridge ideally suited for the study of magmatic processes. To enable this, we generated a three-dimensional gravity model of crustal thickness over the ridge and parts of the adjacent Nansen and Amundsen basins west of 65° E. The model shows that oceanic crust accreted prior to chrons C5/C6 is generally very thin (1–3 km). Magnetic anomalies over this thin crust are highly variable both parallel and perpendicular to the ridge axis. This is the result of amagmatic or weakly volcanic spreading that started with the opening of the basins 56 Ma ago. The separation of Greenland from Svalbard at chron C5/C6 led to the inflow of North Atlantic mantle into the western Eurasia Basin leading to a change in the mantle convection system and the establishment of a magmatic dichotomy along the Gakkel Ridge. Robust magmatism was established in the Western Volcanic Zone (6° 30′ W–3° 30′ E), leading to creation of a 6.6 km thick igneous crust, characterized by a strong positive axial magnetic anomaly, numerous volcanic cones, and widespread thick mid-ocean ridge basalts. The transition to the neighbouring Sparsely Magmatic (3° 30′ E–29° E) and Eastern Volcanic (29° E–85° E) zones is sharp. Peridotites cover the central valley and the inner rift flanks, the central magnetic anomaly vanishes and crustal thickness decreases to 1–4 km. Transverse basement ridges, extending for as much as 100 km into the adjacent basins, intersect the central valley. Although partly of tectonic origin, the transverse ridges are also an expression of long-living magmatic centres, as revealed by increased magnetic anomaly intensities and local thickening of the crust to values as great as 5.9 km.