Abstract Carbonatites, the most silica-poor igneous rocks, have a close relationship with rare earth element (REE) ore deposits, where low SiO2 activity is considered to contribute to economic REE mineralization. However, a paradox is raised by quartz, commonly regarded as a Si-saturation proxy, which occurs in some giant carbonatites or carbonatite-related REE deposits such as those at Bayan Obo, China, and Mountain Pass, California, USA. A unique perception for the origin of quartz in carbonatites is provided here using Si isotope analysis. Quartz grains from the Bayan Obo carbonatite and REE ores commonly occur as inclusions in fluorite, or they coexist with fluorite, thus implicating the importance of fluorine in their hydrothermal origin. The quartz grains have remarkably large variations in δ30Si values, ranging from −4.55‰ to 1.71‰ in secondary ion mass spectrometry analyses, which have not been documented elsewhere in high- to medium-temperature magmatic-hydrothermal processes. Theoretical calculations demonstrate that such large Si isotopic fractionation can be generated during the formation and breakdown of Si-O and Si-F bonds due to their difference in bond strength. These results imply the presence of silicon fluoride species in the fluid and highlight the role of fluorine in quartz formation in silicon-poor carbonatite. The exsolved fluids from carbonatite magmas containing silicon fluoride species may decrease silica activity, which has the potential to impede incorporation of REEs into magmatic apatite, and thus facilitate late-stage hydrothermal REE enrichment and formation of REE orebodies.