The Late Cretaceous orogeny followed by the Eocene collision of the Adriatic with the European plate dissected the Northern Calcareous Alps (NCA) by a number of well-studied strike-slip fault systems accommodating N-S shortening and E-W stretching. However, the post-Miocene fault activity is poorly constrained due to lack of Neogene faulted sediments, and glacial erosion of geomorphic indicators. Using the protected environment of caves, we fill the knowledge gap in the post-Miocene evolution of the NCA by paleostress analysis of 172 reactivated faults that offset passages in 28 caves near major faults. Constrained maximum age of caves, our results indicate that the NCA have been subjected to N to NE trending compression since Pliocene. Faulted speleothems dated with 230Th/U method, indicate that the recorded present-day stress state did not significantly change during the last 0.5 Ma. In contrast to the previously proposed post-Miocene N-S extension of NCA, but in agreement with what was observed in Vienna and Pannonian basins, we conclude that the eastward extrusion resulting from N-S convergence has continued despite a distinct slowdown of plate tectonic velocities in the late Miocene. The N-S extension affected only the Alpine front during Pliocene Molasse basin inversion, while at the scale of the Alpine orogen the NCA underwent successive N-S shortening and E-W stretching.