Caves are ideal environments for preserving quantifiable deformational indicators in orogenic areas, as they are conditioned by regional tectonics. The caves and karst of Isverna, developed in the Barremian-Aptian limestones of the Danubian sedimentary nappes (Southern Carpathians, SW Romania), expose formerly undetected evidence of compressional tectonics, overlapping older structures related to décollement and deformation of the underlying Turonian-Senonian tectonic mélange. The Danubian domain (the distal part of the Moesian Platform) was incorporated into the Carpathian Orogen during the Late Cretaceous subduction of the Ceahlău–Severin Ocean and collision with the continental Dacia mega-unit. Subsequent Eocene–Oligocene orogen–parallel extension led to the development of a metamorphic core complex and detachment faults, constructing a complicated arcuate fault system around the Moesian Platform during the Late Miocene strike-slip deformation. The integrated analysis of structural, kinematic, and geomorphological data indicates a connection between the strike-slip deformation and the subsequent shortening, exhumation and surface exposure of Cerna Nappe within the Isverna shear zone. Four main evolutionary stages of the Danubian thin-skinned units in the central Mehedinți Mountains were distinguished from cave and karst geology, and illustrated in a detailed 3D model: i) Initial décollement and mélange deformation during the Alpine nappe stacking; ii) Extensional décollement toward SE; iii) Dextral shearing and WNW-ESE contraction; iv) Karstification and cave development. Most structural and kinematic markers recorded within the limestones of the Cerna Nappe date from stage (iii), whereas older structures were better preserved in the tectonic mélange of the Lainici Nappe. The resulting model could be further integrated into the polyphase tectonic evolution of the Southern Carpathians and their relation with the Moesian Platform. This study demonstrates the utility of caves and karst for constraining the chronology of tectonic deformations in complex structural systems and for reconstructing more refined conceptual 3D models.