The Saxo-Thuringian zone of the European Variscides contains the record of the Cadomian and Variscan orogenies and a Paleozoic marine transition stage. The classical view of a relatively simple, double-vergent folded sedimentary basin at the end of the Early Carboniferous is challenged by the widespread occurrence of Late Devonian to Early Carboniferous high-pressure metamorphic units tectonically juxtaposed with low-grade Paleozoic successions. Here we demonstrate that the subdivision of the Saxo-Thuringian zone in three principal units (autochthonous domain, wrench and thrust zone, and allochthonous domain) and their heterogeneous overprint by two regional deformation events during the Variscan orogeny explain the entire geological record. Late Devonian to Early Carboniferous subduction of continental crust inside the allochthonous domain affected a Cadomian basement and sediments deposited on the same continental shelf as the one preserved in the autochthonous domain. Strain partitioning during this regional D1 process led to the formation and evolution of a wrench and thrust zone surrounding the autochthonous domain. The latter was only affected by regional D2 deformation, which was related to regional dextral transpression, rapid exhumation of the subducted rocks of the allochthonous domain, and final filling and subsequent folding of the Saxo-Thuringian flysch basin that covers the autochthonous domain and the wrench and thrust zone. The Saxo-Thuringian zone is interpreted as a fragment of Peri-Gondwana that never separated from Gondwana to move as an independent terrane and that borders to the Old Red continent, represented by the Rheno-Hercynian zone, along a strike-slip dominated segment of the Rheic suture. The juxtaposition of the Saxo-Thuringian zone with the adjacent areas is discussed as a continuous subduction and/or accretion process representative for the entire Variscan orogen.