—We present results of petrographic, mineralogical, and geochemical study of all types of rocks of a multiphase pluton and consider the chemical evolution of igneous and metasomatic rocks of the Baga Gazriin Chuluu pluton, based on new precise analytical data. At the early stage of their formation, the pluton granites were already enriched in many trace elements (Li, Rb, Cs, Be, Nb, Ta, Th, and U), F, and HREE relative to the upper continental crust. They show strong negative Ba, Sr, La, and Eu anomalies, which is typical of rare-metal Li–F granites. The geochemical evolution of the Baga Gazriin Chuluu multiphase pluton at the postmagmatic stage was marked by the most intense enrichment of greisens and microclinites with lithophile and ore elements (Sn, W, and Zn) and the formation of ore mineralization. In the permeable rift zone where the Baga Gazriin Chuluu pluton is located, the fluid–magma interaction took place under the impact of a mantle plume. High-temperature mantle fluids caused melting of the crustal substratum, which determined the geochemical specifics of Li–F granite intrusions. Genesis of granitic magma enriched in Li, F, Rb, Sn, and Ta is possible at the low degrees of melting of the lower crustal substratum. The Baga Gazriin Chuluu pluton formed in the upper horizons of the Earth’s crust, where magma undergoes strong differentiation and the saturation of fluids with volatiles can lead to the postmagmatic formation of metasomatites of varying alkalinity (zwitters (greisens), microclinites, and albitites) producing rare-metal mineralization. By the example of the early Mesozoic magmatism area of Mongolia, it is shown that the formation of granites and associated rare-metal minerals is due to the interaction of mantle fluids with the crustal material and the subsequent evolution of granitic magmas.