Pyroxenite-veined garnet peridotites from the Gföhl Unit of the Moldanubian Zone in the Bohemian Massif provide direct constraints on diverse mechanisms of mantle metasomatism and refertilization driven by a single pulse of melt beneath the Central European Variscides. Here, we provide a detailed study on an intriguing example of this rock association where the garnet peridotites show a fertile character (high Al2O3, CaO, TiO2), corresponding to the subcontinental lithospheric mantle (SCLM). By contrast, their conspicuous LREE depletion and Sr–Nd isotopic signatures (87Sr/86Sr338 ≤ 0.7028; εNd338 ~7.3) are typical of depleted mantle residue after melt extraction. Such signatures reflect transformation of an original refractory protolith (likely harzburgite) to fertile lherzolite through percolation of primitive tholeiitic melts, parental to garnet pyroxenite in veins. The SCLM refertilization is further documented by the whole-rock positive correlation between incompatible elements (Zr, Yb, Sc, V), and trace element composition of clinopyroxene (high Ti/Eu and Ti/Nb) and garnet (elevated ∑REE, Zr, Ti). Trace element and Sr–Nd isotopic systematics of pyroxenites (87Sr/86Sr338 ~0.7025–0.7029; εNd338 ≤ 7.9) correspond to a source of melt similar to the depleted MORB mantle (DMM). Three mechanisms of metasomatism related to the interaction of this melt with the host peridotites were distinguished: (i) stealth metasomatism, reflected by extensive clinopyroxene and garnet crystallization in lherzolite adjacent to pyroxenite veins, (ii) cryptic metasomatism, recorded by lower Mg# values of orthopyroxene and olivine in lherzolite, and (iii) modal metasomatism, resulting in crystallization of amphibole and phlogopite in lherzolite close to the veins. The percolating basaltic melt was hydrous, moderately enriched in fluid-mobile elements (Cs, Rb, Ba, Pb, U, Li). Immiscible liquids, dense Ti-Mg-Fe-rich oxide melt and C-O-H fluid, trapped and crystallized as mono/multiphase solid inclusions in garnet, likely separated from a basaltic melt upon cooling. The lherzolite-pyroxenite interface reveals strong micro-scale element fractionation due to differentiation of a basaltic melt within the percolation channel. Volatile-bearing liquids that segregated from the melts migrating through wall-rock peridotites most likely caused chromatographic enrichment in highly incompatible elements (e.g. LREE) in distal peridotites relative to the LREE-depleted lherzolites adjacent to the veins. The DMM-like affinity of pyroxenites and pressure-temperature estimates for lherzolite (3.9–5.4 GPa/1010–1200 °C) and pyroxenites (2.8–4.2 GPa/860–1020 °C) point towards exhumation-driven SCLM refertilization. This was linked to decompression-induced partial melting of upwelling asthenosphere producing basaltic melts penetrating through and metasomatizing the SCLM beneath the Variscan orogenic belt in Central Europe.