A unique case of low-temperature metamorphic (hydrothermal) overprint of peraluminous, highly evolved rare-metal S-type granite is described. The hidden Dlhá dolina granite pluton of Permian age (Western Carpathians, eastern Slovakia) is composed of barren biotite granite, mineralized Li-mica granite and albitite. Based on whole-rock chemical data and evaluation of compositional variations of rock-forming and accessory minerals (Rb-P-enriched K-feldspar and albite; biotite, zinnwaldite and di-octahedral micas; Hf-(Sc)-rich zircon, fluorapatite, topaz, schorlitic tourmaline), the following evolutionary scenario is proposed: (1) Intrusion of evolved peraluminous melt enriched in Li, B, P, F, Sn, Nb, Ta, and W took place followed by intrusion of a large body of biotite granites into Paleozoic metapelites and metarhyolite tuffs; (2) The highly evolved melt differentiated in situ forming tourmaline-bearing Li-biotite granite at the bottom, topaz-zinnwaldite granite in the middle, and quartz albitite to albitite at the top of the cupola. The main part of the Sn, Nb, and Ta crystallized from the melt as disseminated cassiterite and Nb-Ta oxide minerals within the albitite, while disseminated wolframite appears mainly within the topaz-zinnwaldite granite. The fluid separated from the last portion of crystallized magma caused small scale greisenization of the albitite; (3) Alpine (Cretaceous) thrusting strongly tectonized and mylonitized the upper part of the pluton. Hydrothermal low-temperature fluids enriched in Ca, Mg, and CO2 unfiltered mechanically damaged granite. This fluid-driven overprint caused formation of carbonate veinlets, alteration and release of phosphorus from crystal lattice of feldspars and Li from micas, precipitating secondary Sr-enriched apatite and Mg-rich micas. Consequently, all bulk-rock and mineral markers were reset and now represent the P-T conditions of the Alpine overprint.