The genesis of primitive arc magmas has had a major impact on continent formation through time, but the rarity of exposures of deep arc sections limits our understanding of the details of melt migration and differentiation. Abundant pyroxenites are exposed within a 600 m thick section of arc-related mantle harzburgites and dunites in the Herbeira massif of the Cabo Ortegal Complex, Spain. We report a combination of field and petrographic observations with in situ and whole-rock geochemical studies of these pyroxenites. After constraining the effects of secondary processes (serpentinization, fluid or melt percolation and amphibolitization), we determine that the low Al content of pyroxenes, high abundance of compatible elements and the absence of plagioclase reflect melt–peridotite interaction and crystal segregation from primitive hydrous melts at relatively low pressure (<1·2 GPa). Olivine clinopyroxenites and olivine websterites preserving dunite lenses (type 1 and 3 pyroxenites) represent the products of partial replacement of peridotites at decreasing melt/rock ratio following the intrusion of picritic melts. Massive websterites (type 2) may represent the final products of this reaction at higher melt/rock ratios. They crystallized from more Si-rich (boninitic) melts, potentially generated through differentiation of the initially picritic melts or intruded as dykes and veins. Rare opx-rich websterites (type 4) were produced by interaction of these melts with dunites. Chromatographic re-equilibration accompanied late-magmatic crystallization of amphibole from migrating or trapped residual melts. This percolative fractional crystallization produced a range of rare earth element (REE) patterns from spoon-shaped in type 1 pyroxenites to strongly light REE (LREE)-enriched in type 2 and 3 pyroxenites. Particularly high CaO/Al2O3 ratios (2·2–11·3) and the selective enrichment of large ion lithophile elements (LILE) over high field strength elements (HFSE) in Cabo Ortegal pyroxenites suggest the generation of Ca-rich picritic–boninitic parental melts via low-degree, second-stage melting of a refractory lherzolite at <2 GPa, following percolation of slab-derived fluids and/or carbonatite melts. Pyroxenites and their host peridotites record high-temperature deformation followed by the development of sheath folds and mylonites. Peak metamorphism was then reached under eclogite-facies conditions (1·6–1·8 GPa and 780–800°C) as recorded by undeformed garnet coronas around spinel. We suggest that this episode corresponds to the delamination of an arc root owing to gravitational instabilities arising from the presence of abundant pyroxenites within mantle harzburgites. Retrograde metamorphism and hydration under amphibolite-facies conditions were recorded by abundant post-kinematic amphibole, which corresponds to the exhumation of the arc root after its intrusion into a subduction zone. The Cabo Ortegal Complex thus preserves a unique section of delaminated arc root, providing evidence for the significant role of melt–peridotite interaction during the differentiation of primitive arc magmas at depth.