The cratonic part of Greenland has been a hotspot of scientific investigation since the discovery of some of the oldest crust on Earth and of significant diamond potential in the underlying lithospheric mantle, the characterization of which remains, however, incomplete. We applied a detailed petrographic and in situ analytical approach to a new suite of fresh kimberlite-borne peridotite xenoliths, recovered from the North Atlantic craton in SW Greenland, to unravel the timing and nature of mantle metasomatism, and its link to the formation of low-volume melts (e.g. kimberlites) and to geophysically detectible discontinuities. Two types of mineralogies and metasomatic styles, occurring at two depth intervals, are recognized. The first type comprises lherzolites, harzburgites and dunites, some phlogopite-bearing, which occur from ∼100–170 km depth. They form continuous trends towards lower mineral Mg# at increasing TiO2, MnO and Na2O and decreasing NiO contents. These systematics are ascribed to metasomatism by a hydrous silicate melt precursor to c. 150 Ma kimberlites, in the course of rifting, decompression and lithosphere thinning. This metasomatism was accompanied by progressive garnet breakdown, texturally evident by pyroxene–spinel assemblages occupying former coarse grains and compositionally evident by increasing concentrations of elements that are compatible in garnet (Y, Sc, In, heavy rare earth elements) in newly formed clinopyroxene. Concomitant sulphide saturation is indicated by depletion in Cu, Ni and Co. The residual, more silica-undersaturated and potentially more oxidizing melts percolated upwards and metasomatized the shallower lithospheric mantle, which is composed of phlogopite-bearing, texturally equilibrated peridotites, including wehrlites, showing evidence for recent pyroxene-breakdown. This is the second type of lithology, which occurs at ∼90–110 km depth and is inferred to have highly depleted protoliths. This type is compositionally distinct from lherzolites, with olivine having higher Ca/Al, but lower Al and V contents. Whereas low Al may in part reflect lower equilibration temperatures, low V is ascribed to a combination of intrinsically more oxidizing mantle at lower pressure and oxidative metasomatism. The intense metasomatism in the shallow cratonic mantle lithosphere contrasts with the strong depletion recorded in the northwestern part of the craton, which at 590–550 Ma extended to >210 km depth, and suggests loss of ∼40 km of lithospheric mantle, also recorded in the progressive shallowing of magma sources during the breakup of the North Atlantic craton. The concentration of phlogopite-rich lithologies in a narrow depth interval (∼90–110 km) overlaps with a negative seismic velocity gradient that is interpreted as a mid-lithospheric discontinuity beneath western Greenland. This is suggested to be a manifestation of small-volume volatile-rich magmatism, which paved the way for Mesozoic kimberlite, ultramafic lamprophyre, and carbonatite emplacement across the North Atlantic craton.