We report petrography, mineralogy, major- and trace-element compositions of a rare selection of spinel- and garnet-bearing peridotite xenoliths and single crystals separated from peridotites hosted in the Mesoproterozoic Wajrakarur kimberlites from the Eastern Dharwar craton (EDC), India. These ultramafic xenoliths consist of olivine (modal 74–82 vol. %) with Fo92–93, clinopyroxene, orthopyroxene, spinel, garnet, and/or ilmenite. Calculated equilibrium pressure and temperature conditions are 2.5–5.0 GPa and 710–1179 °C for these peridotites, which suggests residence depths >160 km near the base of the Dharwar cratonic lithospheric mantle. Garnet in these ultramafic rocks [with Mg# = molar (Mg/(Mg + Fetotal) × 100 of 80–88] displays either “sinuous” LREE-enriched patterns with depletion in Gd and Er for harzburgites or “normal” LREE-depleted, HREE-enriched patterns for lherzolites. Two groups of clinopyroxenes (group-I and group-II) were also observed with high LREE (LaN > 10) and low LREE (LaN < 10), respectively. The Yb vs. Zr contents in peridotitic garnet are characterised by two distinct trends: one with low-T metasomatism for harzburgitic garnets and the other with high-T metasomatism for lherzolitic garnet, which suggests metasomatism from fluids circulating with in the continental lithospheric mantle, resulting in refertilization from harzburgite to lherzolite. REE concentrations of hypothetical melts calculated to be in equilibrium with peridotitic garnet resemble small volume carbonated silicate melts closely similar to natural kimberlite and lamproites from the Dharwar craton. Modeling suggest that olivine-rich peridotites of the Dharwar craton are the residues of after ~35–50% of melt extraction at ~1500–1540 °C and ≤ 2.0 GPa (≤60 km depth). Residues of these high-Mg# (~92–93) peridotites were generated by shallow and a hot plume melting environment. These processes formed a thick depleted mantle residue of primordial cratonic nucleus of Eastern and Western Dharwar. Later, these two blocks collided and were amalgamated, which further thickened the lithospheric mantle beneath the Dharwar craton. The peridotites later were subjected to metasomatic modification, possibly related to proto-kimberlite activity prior to being transported to the surface by the Mesoproterozoic Wajrakarur kimberlites.