We exploit the data from five seismic transects deployed across the Pyrenees to characterize the deep architecture of this collisional orogen. We map the main seismic interfaces beneath each transect by depth migration of P-to-S converted phases. The migrated sections, combined with the results of recent tomographic studies and with maps of Bouguer and isostatic anomalies, provide a coherent crustal-scale picture of the belt. In the Western Pyrenees, beneath the North Pyrenean Zone, a continuous band of high density/velocity material is found at a very shallow level (~10 km) beneath the Mauleon basin and near Saint-Gaudens. In the Western Pyrenees, we also find evidence for northward continental subduction of Iberian crust, down to 50-70 km depth. In the Eastern Pyrenees, these main structural features are not observed. The boundary between these two domains is near longitude 1.3 °E, where geological field studies document a major change in the structure of the Cretaceous rift system, and possibly a shift of its polarity, suggesting that the deep orogenic architecture of the Pyrenees is largely controlled by structural inheritance.