The Early Cretaceous Baerzhe deposit in Inner Mongolia, Northeast China, hosts a world-class resource of rare earth elements (REEs), niobium, zirconium, and beryllium. In contrast to previous interpretations of the deposit as a multiphase, miaskitic alkaline granite, our observations of the relationships of various rock phases, the textural features and chemical evolution of amphibole, and the distribution of primary and secondary mineral assemblages suggest that the igneous phases evolved from a hypersolvus porphyritic granite, through a variably altered transsolvus granite, both of which are miaskitic, to a strongly altered, agpaitic, transsolvus granite that contained primary elpidite. All of these phases share a common igneous lineage. The Baerzhe deposit is characterized by five stages of rare metal mineralization, starting with the magmatic crystallization of elpidite (stage I). Elpidite was subsequently hydrothermally replaced by zircon and quartz to form pseudomorphs in stage II. Stage II is also characterized by Na metasomatism (albite and aegirine alteration of alkali feldspar and amphibole, respectively) and by snowball quartz that contains inclusions of albite, aegirine, and zircon. Sodium metasomatism, Zr mineralization, and snowball quartz are restricted to the agpaitic rocks. REEs, Nb, and Be occur as a variety of minerals that are disseminated through all the altered rocks and were precipitated in three sequential stages (stages III-V), with the formation of heavy REE-dominant phases generally preceding light REE-dominant phases. Moderate to pervasive hematization, which altered much of the transsolvus miaskitic granite and all the agpaitic granite, initiated late in stage II and accompanied most of the REE-Nb-Be mineralization in stage III. The stage-III mineralization, represented by hingganite-(Y), hingganite-(Ce), aeschynite-(Y), and columbite-(Fe), developed in two substages, with hingganite-(Y) preceding hingganite-(Ce); these REE-Nb-Be minerals are mainly contained in quartz-rich pseudomorphs (REE-Nb-Be–rich pseudomorphs) but also occur as partial replacement of earlier minerals. Stages IV and V represent a transition from F-absent assemblages that are characterized by euxenite-group minerals and monazite-(Ce) in stage IV-A, to light REE and F-rich minerals: bastnäsite-(Ce) in stage IV-B and fluocerite-(Ce) and synchysite-(Ce) in stage V. The low REE, Nb, and Be concentrations in amphibole and the fact that REE-Nb-Be assemblages never contain zircon as a constituent preclude leaching of preexisting amphibole or zirconosilicates as significant sources of REEs, Nb, or Be. Rather, these elements may have inherently been present in magmatic-hydrothermal fluids or have been leached from crystallized fluoride melts.