A structural and geochronological 40Ar/39Ar study was performed in kilometre-scale middle and lower crustal lens-shaped domains dominated by a preserved subvertical foliation, surrounded by horizontally foliated migmatites. These domains occur within the Moldanubian nappe overlying the Brunia microcontinent at the eastern margin of the European Variscides. Three main deformation phases were recognized: subvertical S2 fabric trending NW–SE in lower crustal rocks and NE–SW in mid-crustal rocks. It is reworked by HT/MT horizontal fabric S3 along margins of crustal domains and in surrounding migmatites. S3 bears a prolate NE lineation parallel to the S2–S3 intersection in the lower crustal domain. In the middle crustal units, L3 is weak, connected to oblate strain and trends NE–SW parallel to the S2–S3 intersection. D4 non-coaxial shear deformation is mainly localized at the boundary between the Moldanubian nappe and Brunia and bears strong top to the NNE shear criteria. In order to constrain kinematics of the D3 deformation, strain modelling was performed to show that the Moldanubian hot nappe was frontally thrust over the Brunia indentor. The renewed D4 tangential movement only heterogeneously reactivates the horizontal S3. This evolution is recorded in 40Ar/39Ar amphibole cooling ages, which show two statistically significant Carboniferous peaks at ~342 and 332 Ma, which are also reflected by published detrital muscovite 40Ar/39Ar ages in the adjacent foreland basin. This geochronological record is correlated with progressive erosion of the topographically elevated upper crustal part of the Moldanubian nappe during D3 frontal thrusting, followed by greenschist facies D4 transpressive reactivation and subsequent erosion of high-grade parts of the nappe.