Ultramafic-alkaline-carbonatite complexes (UACC), which are formed from mantle-derived carbonated alkali-ultramafic melts in large igneous provinces (LIPs), are important resources of Fe, Ti, U, Th, Nb, rare earth elements (REEs), Cu, Ni and platinum group elements (PGEs). Concentration of these metals and ore formation is assumed to be largely controlled by magmatic differentiation and post-magmatic hydrothermal processes. Although basic patterns of the metals’ partitioning during formation of the UACCs are constrained by geochemical and mineralogical features of the rocks, including in experimental studies, our understanding of their pathway “from primitive melt to ore deposit” is far from complete. In order to further constrain the metals’ behavior during differentiation of a carbonated alkali-ultramafic melt, we studied multiphase inclusions in olivine, chromite, perovskite, pyroxene and magnetite in the ultramafic rocks from three UACCs (Guli, Bor-Uryakh and Odikhincha), located in the Siberian LIP. Examination of both unheated and experimentally heated and quenched inclusions reveals a variety of compositions from melanephelinitic through to highly differentiated nephelinitic to alkali-rich carbonatitic. In addition, sulfide minerals, which turn into immiscible sulfide liquids during heating experiments, are widely distributed in the inclusions’ assemblages. We consider these inclusions to be snapshots of intercumulus melts, which were entrained into olivine-rich cumulate mush, and use their compositions to delineate plutonic differentiation of a carbonated alkali-ultramafic melt. Highly differentiated silicate melts, entrapped in Fe-rich chromite (Guli dunites), were rich in U, Th and Nb and crystallized Os-Ir-Ru phases in proximity to the host chromite. Concentrations of U, Th, Nb and REEs in alkali-rich carbonatite liquids, which were present in the intercumulus of Odikhincha and Bor-Uryakh peridotites, approached levels similar to mineralized carbonatites and support the concentration of these metals in an immiscible alkali-carbonatite fraction, which was enriched in S, P and Cl. Minor sulfide liquids, which are closely associated with these carbonatite fractions, were strongly enriched in Cu and Ni, thus explaining the origin of the Phalaborwa-like sulfide ores in carbonatites as a result of magmatic differentiation. Finally, our study provides insights into the formation of peridotite-hosted types of mineralization (perovskite-magnetite ores, mineralized carbonatite veins and PGE-bearing chromitites) and shows that these ore-bearing assemblages can be formed due to the infiltration of the metal-bearing intercumulus melts through the ultramafic matrix.