We investigated rare earth element (REE) minerals in low- to medium-grade metapelites sampled in two nappes of the Austroalpine Unit (Eastern Alps, Austria). Combining microstructural and chemical characterization of the main and REE minerals with thermodynamic forward modeling, Raman spectroscopy on carbonaceous material (RSCM) thermometry and in situ U–Th–Pb dating reveal a polymetamorphic evolution of all samples. In the hanging wall nappe, allanite and REE epidote formed during Permian metamorphism (275–261 Ma, 475–520 °C, 0.3–0.4 GPa). In one sample, Cretaceous (ca. 109 Ma) REE epidote formed at ∼440 °C and 0.4–0.8 GPa at the expense of Permian monazite clusters. In the footwall nappe, large, chemically zoned monazite porphyroblasts record both Permian (283–256 Ma, 560 °C, 0.4 GPa) and Cretaceous (ca. 87 Ma, 550 °C, 1.0–1.1 GPa) metamorphism. Polymetamorphism produced a wide range of complex REE-mineral-phase relationships and microstructures. Despite the complexity, we found that bulk rock Ca, Al and Na contents are the main factor controlling REE mineral stability; variations thereof explain differences in the REE mineral assemblages of samples with identical pressure and temperature (P–T) paths. Therefore, REE minerals are also excellent geochronometers to resolve the metamorphic evolution of low- to medium-grade rocks in complex tectonic settings. The recognition that the main metamorphic signature in the hanging wall is Permian implies a marked P–T difference of ∼250 °C and at least 0.5 GPa, requiring a major normal fault between the two nappes which accommodated the exhumation of the footwall in the Cretaceous. Due to striking similarities in setting and timing, we put this low-angle detachment in context with other Late Cretaceous low-angle detachments from the Austroalpine domain. Together, they form an extensive crustal structure that we tentatively term the “Austroalpine Detachment System”.