Multiscale structural analysis was carried out to explore the sequence of superposed pre-Alpine chloritoid–staurolite–andalusite metamorphic assemblages in the polydeformed Variscan basement of the upper Val Camonica, in the central Southalpine domain. The dominant fabric in the upper Val Camonica basement is the late-Variscan S2 foliation, marked by greenschist facies minerals and truncated by the base of Permian siliciclastic sequences. The intersection with the sedimentary strata defines a Permianage limit on the pre-Alpine tectonometamorphic evolution and exhumation of the Variscan basement. The detailed structural survey revealed that the older S1 foliation was locally preserved in low-strained domains. S1 is a composite fabric resulting from combining S1a and S1b: in the metapelites, S1a was supported by chloritoid, garnet, and biotite and developed before S1b, which was marked by staurolite, garnet, and biotite. S1a and S1b developed at intermediate pressure amphibolite facies conditions during the Variscan convergence, S1a at T = 520–550 °C and P ≃ 0.8 GPa, S1b at T = 550–650 °C and P = 0.4–0.7 GPa. The special feature of the upper Val Camonica metapelites is andalusite, which formed between the late D1b and early D2 tectonic events. Andalusite developed at T = 520–580 °C and P = 0.2–0.4 GPa in pre-Permian times, after the peak of the Variscan collision and before the exhumation of the Variscan basement and the subsequent deposition of the Permian covers. It follows that the upper Val Camonica andalusite has a different age and tectonic significance as compared to that of other pre-Alpine andalusite occurrences in the Alps, where andalusite mostly developed during exhumation of high-temperature basement rocks in Permian–Triassic times.