Plumes are domains where hotter material rises through Earth´s mantle, heating also the moving lithospheric plates and causing thinning or even continental breakup. In particular, the Iceland plume in the NE Atlantic (NEA) could have been instrumental in facilitating the breakup between Europe and Laurentia in the earliest Eocene, 55 Ma. This hypothesis relies on different observations that have not yet been integrated into a quantitative description of the present-day geophysical configuration. Here we show an open access three-dimensional model of the entire NEA crust and upper mantle including the conjugate continental margins of Greenland and Norway, as well as the sheared margins of the northernmost NEA. The model is consistent with available seismic, seismological and gravity data. We propose that high-density/high-velocity anomalies in the crust represent the preserved modifications of the lithosphere in consequence of the plate’s journey over the hot mantle plume. Besides, low-density/low-velocity anomalies in the uppermost mantle would represent the present-day effect of the mantle plume and its interaction with the mid-ocean ridges. Overall, the model indicates that the presence of the plume together with the pre-existing crustal configuration controlled the timing, mechanisms and localization of the NEA breakup.