Global fore- and sub-arc peridotites show paradoxically highly melt-depleted yet silica-enriched (as excess orthopyroxene) compositions, which have been attributed to either silica-enriched mantle sources or metasomatic overprints by silica-rich fluids/melts. Here, we present robust mineralogical evidence from an ophiolitic peridotite suite and thermodynamic modeling suggesting that boninitic melt percolation is a viable manner to induce silica enrichment and keep the ultra-depleted signature in a nascent lithospheric mantle wedge. The co-occurrence of resorbed olivines and euhedral high-Cr# spinels with a boninitic origin enclosed by porphyroblastic orthopyroxenes in these peridotites documents that the primary olivines were partially melted or dissolved along with precipitation of the euhedral spinels and growth of the orthopyroxene through reactions between the depleted peridotites and boninitic melts. Such metasomatism modulates the geochemistry of mantle wedges and can explain the compositional variations observed in the majority of global fore- and sub-arc peridotites and supra–subduction zone ophiolitic counterparts. Lateral assembly of these mantle domains by accretionary orogenesis may contribute to the growth of continental lithosphere and accounts for the existence of melt-depleted yet silica-enriched mantle domains beneath orogens.