To characterize the deep structure of the Klippen Belt, we made magnetotelluric measurements in profiles across the western and eastern segments in the territory of Slovakia, from which we created 3D models. The models revealed significant differences in tectonic structure between these segments. In the western segment, the Klippen Belt is located in the southern reversing wing of the original subduction flower structure (retroarc thrusting) with an overthrust to the south onto the Inner Western Carpathian units. This structure was later modified by significant transpressional movements. In the eastern segment, the Klippen Belt is primarily an organic part of the accretionary wedge of the Outer Western Carpathians and it is overthrusted onto the Flysch Belt. This was followed by modification of the structures, mostly in a transpressional regime, including local reversing overthrusts and the development of a steep fault boundary, mainly along the southern margin, against the Inner Carpathian Paleogene succession. These differences between the structure of the western and eastern Klippen Belt segments indicate the contrast between the interaction of the western and eastern parts of the Inner Western Carpathians with the European Platform. In the western part, oblique collision and sinistral transpression dominate. In the eastern part, by contrast, subduction and orthogonal collision dominated over later transpressional modifications.