Abstract Rare-metal mineralization in aluminous granites (i.e. rare-metal granites, RMGs) is usually associated with high degree of magma fractionation, strong enrichment in fluxing elements (Li, B, P, and F), and the operation of both magmatic and hydrothermal processes. Experimental data have established the theoretical basis for melt- or fluid-driven rare-metal mineralization. To investigate these mechanisms in natural samples, this paper presents detailed textural and compositional variations for zoned micas and rare-metal minerals from rocks of the Late Jurassic Yashan rare-metal granitic pluton, South China. This pluton preserves an evolutionary sequence from ore-barren rocks to those containing ores formed by Ta–Nb–Li mineralization during magmatic–hydrothermal processes. Three main units of the Yashan pluton are exposed: from bottom to top, these comprise protolithionite–muscovite granite (Unit I), Li-mica granite (Unit II), and topaz–lepidolite granite (Unit III), representing crystallization from successive magma batches from a deep-level magma chamber. The gradual decrease in Nb/Ta and K/Rb in both whole rocks and micas from units I to II to III illustrates fractionation within the magma chamber, accompanied by successive enrichment of incompatible elements in the residual melt. Furthermore, the strong enrichment of fluxing elements such as Li, P, and F in Unit III likely led to lower magma viscosity, which may have helped to expulse interstitial residual melt from the magma chamber. Zoned micas from the Yashan pluton are composed of Li-phengite or lepidolite inner cores and muscovite rims. Cores show increasing Li, F, and rare-metal elements from units I and II to Unit III, consistent with the trend of magmatic fractionation. In contrast, rims that formed in the residual hydrosilicate melt show marked decrease in F and rare metals (i.e. Li, Cs, Rb, Nb, Ta, Sn, and W). Chemical variations of the zoned micas and rare-metal minerals were used together with Rayleigh fractionation modeling calculations to reconstruct the contribution of melt–fluid immiscibility to the crystallization of rare metals, which took place via the combination of melts enriched in high-field-strength elements (e.g. Nb and Ta) and fluids enriched in mobile elements (e.g. Mn, Fe, W, and Cs). Strong fractionation of Nb and Ta, along with extreme enrichment of Ta, in RMGs is caused mainly by the crystallization of micas and columbite-group minerals, and also depends on the degree of fractional crystallization. The subsolidus alteration of micas by acidic fluids may have leached some Nb rather than Ta during chloritization, which could have partly contributed to the enrichment of rare metals and fractionation of Nb–Ta. It is concluded that magmatic–hydrothermal processes, including magmatic evolution and fluid exsolution, are critical for rare-metal enrichment and Nb–Ta fractionation in RMGs.