Phase relations are studied experimentally in the harzburgite–hydrous carbonate melt system, the bulk composition of which represents primary kimberlite. Experiments were carried out at 5.5 and 7.5 GPa, 1200–1350°С, and Xco2 = 0.39–0.57, and lasted 60 hours. It is established that olivine–orthopyroxene–garnet–magnesite–melt assemblage is stable within the entire range of the studied parameters. With increase of temperature and Xco2 in the system, Ca# in the melt and the olivine fraction in the peridotite matrix significantly decrease. The composition of silicate phases in run products is close to those of high-temperature mantle peridotite. Analysis of obtained data suggest that magnesite at the base of subcontinental lithosphere could be derived by metasomatic alteration of peridotite by asthenospheric hydrous carbonate melts. The process is possible in the temperature range typical of heat flux of 40–45 mW/m2, which corresponds to the conditions of formation of the deepest peridotite xenoliths. Crystallization of magnesite during interaction with peridotite matrix can be considered as experimentally substantiated mechanism of CO2 accumulation in subcratonic lithosphere.