Abstract The Obnazhennaya kimberlite in the NE Siberian craton hosts a most unusual cratonic xenolith suite, with common rocks rich in pyroxenes and garnet, and no sheared peridotites. We report petrographic and chemical data for whole rocks (WR) and minerals of 20 spinel and garnet peridotites from Obnazhennaya with Re-depletion Os isotope ages of 1.8–2.9 Ga (Ionov et al., 2015a) as well as 2 pyroxenites. The garnet-bearing rocks equilibrated at 1.6–2.8 GPa and 710–1050 °C. Some xenoliths contain vermicular spinel-pyroxene aggregates with REE patterns in clinopyroxene mimicking those of garnet. The peridotites show significant scatter of Mg# (0.888–0.924), Cr2O3 (0.2–1.4 wt.%) and high NiO (0.3–0.4 wt.%). None are pristine melting residues. Low-CaO-Al2O3 (≤0.9 wt.%) dunites and harzburgites are melt-channel materials. Peridotites with low to moderate Al2O3 (0.4–1.8 wt.%) usually have CaO > Al2O3, and some have pockets of calcite texturally equilibrated with olivine and garnet. Such carbonates, exceptional in mantle xenoliths and reported here for the first time for the Siberian mantle, provide direct evidence for modal makeover and Ca and LREE enrichments by ephemeral carbonate-rich melts. Peridotites rich in CaO and Al2O3 (2.7–8.0 wt.%) formed by reaction with silicate melts. We infer that the mantle lithosphere beneath Obnazhennaya, initially formed in the Mesoarchean, has been profoundly modified. Pervasive inter-granular percolation of highly mobile and reactive carbonate-rich liquids may have reduced the strength of the mantle lithosphere leading the way for reworking by silicate melts. The latest events before the kimberlite eruption were the formation of the carbonate-phlogopite pockets, fine-grained pyroxenite veins and spinel-pyroxene symplectites. The reworked lithospheric sections are preserved at Obnazhennaya, but similar processes could erode lithospheric roots in the SE Siberian craton (Tok) and the North China craton, where ancient melting residues and reworked garnet-bearing peridotites are absent. The modal, chemical and Os-isotope compositions of the Obnazhennaya xenoliths produced by reaction of refractory peridotites with melts are very particular (high Ca/Al, no Mg#-Al correlations, highly variable Cr, low 187Os/188Os, continuous modal range from olivine-rich to low-olivine peridotites, wehrlites and websterites) and distinct from those of fertile lherzolites in off-craton xenoliths and peridotite massifs. These features argue against the concept of ‘refertilization’ of cratonic and other refractory peridotites by mantle-derived melts as a major mechanism to form fertile to moderately depleted lherzolites in continental lithosphere. The Obnazhennaya xenoliths represent a natural rock series produced by ‘refertilization’, but include no rocks equivalent in modal, major and trace element to the fertile lherzolites. This study shows that ‘refertilization’ yields broad, continuous ranges of modal and chemical compositions with common wehrlites and websterites that are rare among off-craton xenoliths.