The metamorphic architecture of the Variscan basement in the Tatra Mountains provides evidence for nappe tectonics during Variscan continental collision in the Late Palaeozoic. We reconstruct the metamorphic history of the lower unit using phase equilibrium modelling, zirconium-in-rutile geothermometry and in situ LA-ICP-MS Th–U–Pb monazite geochronology of metapelites. We also present new U–Pb zircon ages from upper unit granitoids. In the lower unit, the peak assemblage in staurolite-kyanite schists is garnet + muscovite + biotite + staurolite + kyanite + plagioclase + rutile + quartz. Structurally higher, a kyanite-fibrolite zone is marked by loss of staurolite and abundant kyanite, commonly replaced by fibrolitic sillimanite. P–T conditions increase from 600–640°C and 6–8 kbar in the staurolite–kyanite zone to 640–655°C and 6.5–8.5 kbar in the kyanite–fibrolite zone. Monazite ages show downward younging from 342–332 Ma in the kyanite–fibrolite zone to 338–315 Ma in the underlying staurolite–kyanite zone, revealing a temporally and structurally inverted metamorphic sequence. These ages are younger than zircon ages in upper unit granitoids (353–346 Ma), indicating prograde metamorphism in the lower unit overlapped with late granitoid intrusion above. The inverted metamorphic sequence and spatially decoupled thermal histories of the upper and lower units suggest that nappe stacking played a dual role: accommodating crustal shortening and driving crustal re-equilibration through partial melting and melt migration. These processes are critical for the long-term rheological evolution of orogenic belts and for understanding the coupling between deformation, metamorphism and plutonism in thickened continental crust.