Comparative analysis of the earlier obtained and new geological data, age, mineral, petrological, and geochemical compositions of plutons of calc-alkalic granitoids and rare-metal Li–F granites shows their evolution in a wide time interval during the formation of Mesozoic areas of granitoid magmatism. Mineralogical and geochemical analysis of the evolution of plutons of palingenetic calc-alkalic granitoids (Baga Hentiyn (MZ1) and Ikh Narotiin = Hiid (MZ2)) and intrusions of rare-metal Li–F granites of Central and Eastern Mongolia revealed their petrological and geochemical differences. The closure of the Mongol–Okhotsk Basin with the formation of large plutons of calc-alkaliс granitoids, obviously related to collisional processes, did not cause significant enrichment of the late granite phases with lithophile and ore elements. Within the peripheral zones of еру MZ1 and MZ2 magmatic areas, mineralization is often associated with Mongolian multiphase plutons and small intrusions of rare-metal Li–F granites. The rare-metal granites are characterized by a decrease in indicative K/Rb, Nb/Ta, and Zr/Hf values and a regular increase in F, Li, Rb, Cs, Sn, W, Be, Ta, and Nb contents during the evolution of Li–F magmas. Igneous and, particularly, metasomatic rocks in most intrusions of ore-bearing rare-metal Li–F granites are characterized by significant variations in Sn and W contents. At the magmatic stage, the pegmatoid varieties of amazonite–albite granites and pegmatites of the zonal Baga Gazriin (MZ1) and Barun Tsogto (MZ2) plutons are significantly enriched in both Sn and W. Maximum Sn and W enrichment has been established in greisenized granites and zoned greisen bodies (zwitters), which is due to the percolation of ore-bearing solutions into the upper horizons and the mineralization of ore elements in the late phases of intrusions and in metasomatites. The wide variations in the age (321–126 Ma) and trace element and isotope compositions of Mongolian rare-metal Li–F granites within various zones of large magmatic areas suggest the influence of mantle plume sources on the composition of rare-metal granitic magmas and on their ore potential in intermediate chambers in the continental crust.