The late Eocene – early Miocene Alpine–Carpathian fold-and-thrust belt (FTB) lies in the transition between the Eastern Alps and the Western Carpathians, SE of the Bohemian crystalline massif. Our study shows the involvement of crystalline basement from the former European Jurassic continental margin in two distinct events. A first extensional event coeval with Eggerian–Karpatian (c. 28–16 Ma) thin-skinned thrusting reactivated the rift basement fault array and resulted from the large degree of lower plate bending promoted by high lateral gradients of lithospheric strength and slab pull forces. Slab break-off during the final stages of collision around Karpatian times (c. 17–16 Ma) promoted large-wavelength uplift and an excessive topographic load. This load was reduced by broadening the orogenic wedge through the reactivation of the lower-plate deep detachment beneath and ahead of the thin-skinned thrust front (with the accompanying positive inversion of the basement fault array) and ultimately, by the collapse of the hinterland summits, enhanced by transtensional faulting. Although this work specifically deals with the involvement of the basement in the Alpine–Carpathian Junction, the main conclusions are of general interest to the understanding of orogenic systems.