Some mantle-derived Kerguelen harzburgite and dunite xenoliths have bulk-rock and mineral trace element compositions that provide evidence of carbonatitic metasomatism similar to that described in some continental and other oceanic settings. Rare xenoliths contain carbonates that are highly enriched in rare earth elements (REE), interpreted to be quenched, evolved carbonatitic melts. One amphibole-bearing dunite mantle wall-rock containing carbonates in small interstitial pockets (100–500 μm across) has been studied in detail. Mg-bearing calcite (MgO: <1.4 wt.%, XCa 0.96) with unusually high REE abundances and strong light REE (LREE) enrichment occurs in the pockets and is sometimes associated with euhedral carbonates (dolomite and Mg-free calcite), mafic silicate glass (low in alkalis) and with fine grains of spinel, sulfides and magnesio–wüstite concentrated near the boundaries of the carbonate pockets. The unusual metasomatic mineral assemblage, together with the microstructural features and chemical composition of carbonates (with trace element contents similar to those of common carbonatite magmas), suggests that the pockets of Mg-bearing calcite represent quenched carbonate melts rather than crystal cumulates from carbonate-rich melts. The associated mafic silicate glass could represent the immiscible silicate fraction of an evolved fluid produced by the dissolution–percolation of the original carbonate melt in the dunitic matrix and subsequent unmixing as the xenoliths ascended to the surface. Clinopyroxene formed during the percolation event and is therefore inferred to be in chemical equilibrium with the carbonate melt. This allowed calculation of clinopyroxene/carbonate melt partition coefficients for a large set of trace elements at relatively low pressure (1 GPa). As a result, a significant pressure control on REE partitioning between carbonate melt and silicate minerals was observed. This study provides further evidence for the occurrence of carbonate melts and demonstrates that these melts can be preserved in hot oceanic uppermost mantle.