The nature of petrogenetic links between carbonatites and associated silicate rocks is a matter of discussion for several decades and still remains controversial among igneous petrologists. The Belaya Zima plutonic complex in southern Siberia is a typical intrusion, in which carbonatites are spatially and temporally associated with the ijolite series rocks and nepheline syenites. In this study we use whole-rock compositions and trace element characteristics of the major and accessory minerals for reconstructing the magmatic evolution of the complex and clarifying the origin of carbonatites. We conclude that the observed gradual increase of Zr, Nb and REE concentrations in the magma is consistent with the process of extensive fractional crystallization and gradual transition from silicate rocks to carbonatites, and inconsistent with the formation of carbonatites by liquid immiscibility. Magma differentiation by fractional crystallization continued during the carbonatite formation. The textural and analytical evidence indicates that the early calcitic carbonatites evolved to dolomitic and ankeritic carbonatites. In addition, maximum Nb and Zr concentrations occur in the calcitic carbonatite, whereas the REE content increases in the dolomitic and ankeritic facies. •Сarbonatites are enriched in Zr, Nb and REE in comparison to alkaline silicate rocks.•Alkaline silicate rocks and carbonatites are related by simple fractional crystallization.•Fractional crystallization was continued during the carbonatite formation.