This work presents the results of an investigation of an assemblage of secondary Sc-minerals from the intraplutonic metaluminous pegmatite Kožichovice II, Třebíč Pluton, Czech Republic. The assemblage was formed by hydrothermally-induced dissolution of primary Sc-enriched (≈1.6 wt.% Sc2O3) columbite-(Mn) followed by in situ reprecipitation of volumetrically dominant fersmite (≈0.16 wt.% Sc2O3) and minor nioboheftetjernite (ScNbO4). Subsequent hydrothermal processes resulted in the formation of fluorcalciomicrolite + Sc-minerals (thortveitite + kristiansenite) + titanite. The mass balance calculations (based on EPMA-derived mineral compositions, mineral proportions obtained from TIMA automated mineralogy and textural observations) revealed that the amount of Sc released from the replaced mass of columbite-(Mn) is significantly higher than the amount of Sc incorporated in the mass of the secondary minerals. This indicates that part of the Sc was mobilised and released to the host rocks (pegmatite and granite). The secondary mineral assemblages indicate elevated Ca activity in the alteration fluids. Other occurrences of Sc-minerals in pegmatites (Baveno Pluton and Heftetjern pegmatite) show remarkable similarities in the paragenetic position of Sc-minerals (late hydrothermal/replacement minerals), including the high activity of Ca in fluids during their formation. The high activity of Ca in fluids during the metasomatic replacement of Sc-enriched precursors causes the formation of the volumetrically dominant Sc incompatible phases, followed by a local supersaturation of Sc resulting in the crystallisation of secondary Sc-minerals.