Indentation of rigid blocks into rheologically weak orogens is generally associated with spatiotemporally variable vertical and lateral block extrusion. The European Eastern and Southern Alps are a prime example of microplate indentation, where most of the deformation was accommodated north of the crustal indenter within the Tauern Window. However, outside of this window only the broad late-stage exhumation pattern of the indented units as well as of the indenter itself is known. In this study we refine the exhumational pattern with new (U–Th–Sm)/He and fission-track thermochronology data on apatite from the Karawanken Mountains adjacent to the eastern Periadriatic fault and from the central-eastern Southern Alps. Apatite (U–Th–Sm)/He ages from the Karawanken Mountains range between 12 and 5 Ma and indicate an episode of fault-related exhumation leading to the formation of a positive flower structure and an associated peripheral foreland basin. In the Southern Alps, apatite (U–Th–Sm)/He and fission-track data combined with previous data also indicate a pulse of mainly Late Miocene exhumation, which was maximized along thrust systems, with highly differential amounts of displacement along individual structures. Our data contribute to mounting evidence for widespread Late Miocene tectonic activity, which followed a phase of major exhumation during strain localization in the Tauern Window. We attribute this exhumational phase and more distributed deformation during Adriatic indentation to a major change in boundary conditions operating on the orogen, likely due to a shift from a decoupled to a coupled system, possibly enhanced by a shift in convergence direction.