We report the concentrations ([Li]) and isotopic compositions of Li in mineral separates and bulk rocks obtained by MC-ICPMS for 14 previously studied garnet and spinel peridotite xenoliths from the Udachnaya kimberlite in the central Siberian craton as well as major and trace element compositions for a new suite of 13 deformed garnet peridotites. The deformed Udachnaya peridotites occur at > 5 GPa; they are metasomatized residues of melt extraction, which as a group experienced greater modal and chemical enrichments than coarse peridotites. We identify two sub-groups of the deformed peridotites: (a) mainly cryptically metasomatized (similar to coarse peridotites) with relatively low modal cpx (< 6%) and garnet (< 7%), low Ca and high Mg#, sinusoidal REE patterns in garnet, and chemically unequilibrated garnet and cpx; (b) modally metasomatized with more cpx and garnet, higher Ca, Fe and Ti, and equilibrated garnet and cpx. The chemical enrichments are not proportional to deformation degrees. The deformation in the lower lithosphere is caused by a combination of localized stress, heating and fluid ingress from the pathways of ascending proto-kimberlite melts, with metasomatic media evolving due to reactions with wall rocks. Mg-rich olivine in spinel and coarse garnet Udachnaya peridotites has 1.2–1.9 ppm Li and δ7Li of 1.2–5.0‰, i.e. close to olivine in equilibrated fertile to depleted off-craton mantle peridotites from literature data, whereas olivine from the deformed peridotites has higher [Li] (2.4–7.5 ppm) and a broader range of δ7Li (1.8–11.6‰), which we attribute to pre-eruption metasomatism. [Li] in opx is higher than in coexisting olivine while Δ7LiOl-Opx (δ7LiOl − δ7LiOpx) ranges from − 6.6 to 7.8‰, indicating disequilibrium inter-mineral [Li] and Li-isotope partitioning. We relate these Li systematics to interaction of lithospheric peridotites with fluids or melts that are either precursors of kimberlite magmatism or products of their fractionation and/or reaction with host mantle. The melts rich in Na and carbonates infiltrated, heated and weakened wall-rock peridotites to facilitate their deformation as well as produce high [Li] and variable, but mainly high, δ7Li in olivine. The carbonate-rich melts preferentially reacted with the opx without achieving inter-mineral equilibrium because opx is consumed by such melts, and because of small volumes and uneven distribution of the metasomatic media, as well as short time spans between the melt infiltration and the capture of the wall-rock fragments by incoming portions of ascending kimberlite magma as xenoliths. Trapped interstitial liquid solidified as cryptic components responsible for high [Li] and the lack of δ7Li balance between olivine and opx, and bulk rocks. Unaltered δ26Mg values (0.20–0.26‰) measured in several olivine separates show no effects of the metasomatism on Mg-isotopes, apparently due to high Mg in the peridotites.