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Abstract The discrepancy between Na-rich compositions of modern carbonatitic lavas (Oldoinyo Lengai volcano) and alkali-poor ancient carbonatites remains a topical problem in petrology. Although both are supposedly considered to originate via fractional crystallization of a “common parent” alkali-bearing Ca-carbonatitic magma, there is a significant compositional gap between the Oldoinyo Lengai carbonatites and all other natural compositions reported (including melt inclusions in carbonatitic minerals). In an attempt to resolve this, we investigate the petrogenesis of Ca-carbonatites from two occurrences (Guli, Northern Siberia and Tagna, Southern Siberia), focusing on mineral textures and alkali-rich multiphase primary inclusions hosted within apatite and magnetite. Apatite-hosted inclusions are interpreted as trapped melts at an early magmatic stage, whereas inclusions in magnetite represent proxies for the intercumulus environment. Melts obtained by heating and quenching the inclusions, show a progressive increase in alkali concentrations transitioning from moderately alkaline Ca-carbonatites through to the “calcite CaCO3 + melt = nyerereite (Na,K)2Ca2(CO3)3” peritectic, and finally towards Oldoinyo Lengai lava compositions. These results give novel empirical evidence supporting the view that Na-carbonatitic melts, similar to those of the Oldoinyo Lengai, may form via fractionation of a moderately alkaline Ca-carbonatitic melt, and therefore provide the “missing piece” in the puzzle of the Na-carbonatite’s origin. In addition, we conclude that the compositions of the Guli and Tagna carbonatites had alkali-rich primary magmatic compositions, but were subsequently altered by replacement of alkaline assemblages by calcite and dolomite.