Economic concentrations of rare earth element (REE) minerals are uncommon in the Earth’s crust, with most occurring in carbonatites. Unlike most igneous rocks composed of silicate minerals, carbonatites are dominated by carbonate minerals, some of which can incorporate significant light REEs (LREEs; La, Ce, Pr, Nd). Technological applications of REEs are numerous and they have been identified as some of the most critical mineral commodities to the global economy. The Mountain Pass carbonatite stock in the Mojave Desert of California is the most economically significant REE deposit in the USA and contains a few to tens of percent (by volume) of the carbonate REE ore mineral bastnäsite. Despite the economic significance of the Mountain Pass deposit, studies of its ore mineralogy are limited. Here we present new carbonate ore mineralogy data for a compositionally diverse suite of carbonatitic rocks from the Mountain Pass stock and related dikes. Whole-rock geochemical data are integrated with mineral-scale textural and chemical data obtained by scanning electron microscopy (SEM), electron probe microanalysis (EPMA), and microRaman spectroscopy. Our results document a complex spectrum of REE-bearing carbonate minerals and intermediate mixed-layer structures. Mineral species include bastnäsite [REE(CO₃)F], hydroxylbastnäsite [REE(CO₃)OH], parisite [Ca(REE)₂(CO₃)₃F₂], synchysite [Ca(REE)(CO₃)₂F], röntgenite [Ca₂(Ce,La)₃(CO₃)₅F₃], and sahamalite [(Mg,Fe²⁺)(REE)₂(CO₃)₄]. Carbonate ore mineralogy is heterogeneous within and between samples, including at the intracrystal scale. Complexly zoned crystals exhibit as many as five to six different compositional domains and syntaxial intergrowths, commonly with the more Ca-rich varieties (parisite, synchysite) forming crystal rims that surround relict bastnäsite cores. We attribute the phenocryst variability to changes in the chemistry and temperature of primary carbonatite magmas and evolved/exsolved fluids. Cross-cutting vein textures of calcite, celestine and various REE carbonate minerals, interstitial bastnäsite crystallization, breccia blocks lined by fine-grained bastnäsite, and the presence of hydroxylbastnäsite and partially hydroxylated bastnäsite point to the role of secondary hydrothermal processes in REE mineralization. Fluorcarbonate mineral compositions demonstrate that La and Ce are more structurally abundant in bastnäsite, whereas the more Ca-rich species (parisite, synchysite) contain a greater proportion of REE heavier than Pr (Nd, Sm, Eu, Gd) and Y. Atomic ratios of Pr/(Nd + Pr) are likewise variable, with the highest average value for bastnäsite (0.25) compared to parisite (0.22) and sychysite (0.21). This finding has geometallurgical implications, given that current mining operations are focused on recovery of Nd and Pr for high field strength permanent magnets and the Nd/Pr ratios are a critical factor in ore processing and magnet manufacture.