High-silica granites are hypothesized to form via fractionation in the shallow crust, yet the predicted residues are rarely identified and can be difficult to distinguish within plutons whose rocks otherwise plot along liquid lines of descent. Bulk-rock compositional mass balance in the late Miocene Risco Bayo–Huemul plutonic complex (Chile) suggests that lithological differences within the Huemul pluton reflect residual crystal concentration in response to melt extraction. A compositional gap from 70 to 75 wt% SiO2 and strong depletion in Ba and Eu suggest that Huemul alkali feldspar (Afs) granites are frozen remnants of highly evolved rhyolitic melt extracted from a mush. Quartz monzonites enriched in Zr and Ba with Eu/Eu* near unity are interpreted to represent the complementary residual silicic cumulates of this fractionation process. Compositional variations in Afs granite zircon (Eu/Eu*, Dy/Yb) further support extraction of this melt from a zircon-saturated mush. U-Pb zircon dates indicate that Huemul rocks evolved ∼800 k.y. after initial crystallization of more mafic Risco Bayo rocks, likely precluding their evolution via fractionation from mafic forerunners. This pluton records a means to produce rhyolite in the upper crust, which has propelled large silicic eruptions during the Quaternary within the Andean subduction zone.