The Basque-Cantabrian junction corresponds to an inverted rift accommodation zone at the limit between the former hyperextended Pyrenean and Cantabrian rift segments. The recognition of an inherited rift segment boundary allows to investigate the reactivation associated with large-scale rift segmentation in an orogenic system. We use criteria from published field observations and seismic data to propose a new map of rift domains for the Basque-Cantabrian junction. We also provide balanced crosssections that allow to define the along-strike architecture associated with segmentation during rifting and subsequent Alpine reactivation. Based on these results, this study aims to characterize and identify reactivated and newly formed structures during inversion of two rift segments and its intermitted segment boundary. It also aims to describe the timing of thinskinned and thickskinned deformation associated with the inversion of segmented rift systems. During convergence, two phases have been recognized within the rift segment (eastern Mauléon basin). The Late Cretaceous to Paleocene underthrusting/subduction phase was mostly governed by thinskinned deformation that reactivated the former hyperextended domains and the supra-salt sedimentary cover. The Eocene to Miocene collisional phase, controlled by thickskinned deformation that took place once necking domains collided and formed an orogenic wedge. At the rift segment boundary, the underthrusting/subduction phase was already controlled by thickskinned deformation due to the formation of shortcutting thrust faults at the termination of overlapping Vshaped rift segments. This led to the formation of a proto-wedge composed of the Basque massifs. We suggest that this proto-wedge is responsible for the preservation of pre-Alpine structures in the Basque massifs and for the emplacement of subcontinental mantle rocks at a crustal level beneath the western Mauléon basin. These results argue for a first order cylindrical orogenic architecture from the Central Pyrenean segment to the Cantabrian segment (up to the Santander transfer zone) despite rift segmentation. They also highlight the control of 3D rift-inheritance for the initial phase of orogenic evolution and for the local architecture of mountain belts.