The Middle Paleoproterozoic (1.99 Ga) Tiksheozero ultramafic‒alkaline‒carbonatite complex in Northern Karelia is one of the Earth’s oldest alkaline complexes. The major and trace-element compositions of minerals were used to decipher the genetic relations between ultramafic cumulates, alkaline rocks, and carbonatites. Based on detailed analysis of clinopyroxenes from ultramafic cumulates, it was assumed that they were derived from an alkaline melt. It was estimated that ultramafic cumulates and alkaline rocks were formed at close moderate pressure, which in combination with the above facts, is consistent with their cogenetic origin. The REE patterns of clinopyroxenes are characterized by the high LREE/HREE fractionation, with slightly convex-upward LREE patterns (La/Nd < 1), which are typical of deep-seated cumulates formed in an equilibrium with an alkaline basaltic melt. Two types of REE zoning were distinguished in apatite using cathodoluminescence imaging. The first type with an outward LREE decrease was found in apatite from silicate rocks of the complex and was likely produced by the closed-system overgrowth of apatite from a residual melt at the late magmatic stage. In contrast, apatite from carbonatite is characterized by a slight outward LREE increase, which is likely related to the re-equilibration of apatite with fresh batches of REE-enriched carbonatite magma. Precipitation of monazite along fractures and margins of apatite in complex with essential HREE and Y enrichment observed in syenite is indicative of the metasomatic interaction of this rock with fluid. Apatites from alkaline rocks and carbonatites define a common trend in the Y–Ho diagram, with a decrease in the Y/Ho ratio from foidolites to carbonatites. This fact together with the absence of signs of liquid immiscibility, and compositional variations in apatite in silicate rocks and carbonatites, are consistent with their origin through fractional crystallization rather than liquid immiscibility.