The Miocene deformation history of magmatic and host metamorphic rocks and surrounding sediments was reconstructed by measuring meso-and microscale structures and anisotropy of magnetic susceptibility (AMS) data in order to constrain the structural evolution of the Pohorje pluton during the onset of lithospheric extension at the Eastern Alps-Pannonian Basin transition. Principal AMS axes, lineation and foliation are very similar to mesoscopic lineation and foliation data from the main intrusive body and from some dykes. Although contribution from syn-magmatic texture is possible, these structures were formed during the cooling of the pluton and associated subvolcanic dykes just shortly after the 18.64 Ma pluton intrusion. Dykes emplaced during progressively younger episodes reflect decreasing amount of ductile strain, while firstly mesoscopic foliation and lineation, and then the tectonic AMS signal gradually disappears. In the structurally highest N-S trending dacite dykes, the AMS fabric only reflects the magmatic flow. The Miocene sediments underwent the same, NE-SW to E-W extension as the magmatic and host metamorphic rocks as indicated by both AMS and fault-slip data. All these events occurred prior to ~ 15 Ma, i.e., during the main syn-rift extension of the Pannonian Basin and during the fastest exhumation of the Tauern and Rechnitz windows, both demonstrating considerable extension of diverse crustal segments of the Alpine nappe pile. After a counterclockwise rotation around ~ 15 Ma, the maximum stress axis changed to a SE-NW orientation, but it was only registered by brittle faulting. During this time, the overprinting of a syn-rift extensional AMS texture was not possible in the cooled or cemented magmatic, metamorphic and sedimentary rocks.