Spinel peridotite xenoliths in alkali basalts at Tok, SE Siberian craton range from fertile lherzolites to harzburgites and wehrlites; olivine-rich (70–84%) rocks are dominant. REE patterns in the lherzolites range from nearly flat for fertile rocks (14–17% cpx) to LREE-enriched; the enrichments are positively correlated with modal olivine, consistent with high-permeability of olivine-rich rocks during melt percolation. Clinopyroxene in olivine-rich Tok peridotites typically has convex-upward trace element patterns (La/NdPM < 1 and Nd/YbPM ≫ 1), which we consider as evidence for equilibration with evolved silicate liquids (with higher REE and lower Ti contents than in host basalts). Whole-rock patterns of the olivine-rich xenoliths range from convex-upward to LREE-enriched (La/NdPM > 1); the LREE-enrichments are positively correlated with phosphorus abundances and are mainly hosted by accessory phosphates and P-rich cryptocrystalline materials. In addition to apatite, some Tok xenoliths contain whitlockite (an anhydrous, halogen-poor and Na–Mg-rich phosphate), which is common in meteorites and lunar rocks, but has not been reported from any terrestrial mantle samples. Some olivine-rich peridotites have generations of clinopyroxene with distinct abundances of Na, LREE, Sr and Zr. The mineralogical and trace element data indicate that the lithospheric mantle section represented by the xenoliths experienced a large-scale metasomatic event produced by upward migration of mafic silicate melts followed by percolation of low-T, alkali-rich melts and fluids. Chromatographic fractionation and fractional crystallisation of the melts close to the percolation front produced strong LREE-enrichments, which are most common in the uppermost mantle and are related to carbonate- and P2O5-rich derivatives of the initial melt. Reversal and gradual retreat of the percolation front during thermal relaxation to ambient geotherm (“retrograde” metasomatism) caused local migration and entrapment of small-volume residual fluids and precipitation of volatile-rich accessory minerals. A distinct metasomatic episode, which mainly produced “anhydrous” late-stage interstitial materials was concomitant with the alkali basaltic magmatism, which brought the xenoliths to the surface.