Fluorapatite-amphibole-magnetite assemblages are a signature alteration product in iron oxide alkali-calcic alteration (IOAA) systems that can host iron oxide-apatite (IOA) and iron oxide Cu-Au (IOCG) deposits. The distinct fluorapatite chemistry that evolves within these systems can record metasomatic processes within IOA and IOCG deposits. Rare earth element (REE)-rich fluorapatite forms during high-temperature sodic-calcic-ferric/ferrous and calcic-ferric/ferrous metasomatism. As temperature declines and the fluid chemistry evolves, localized REE leaching takes place within fluorapatite and leads to secondary allanite and monazite crystallization. Such processes have been observed experimentally and inferred in IOA deposits (e.g., Kiruna district in Sweden, Bafq district in Iran). In the present study, fluorapatite grains in thin section and hand-picked from disaggregated bedrock samples from a number of areas including the Fab system, Brooke Zone, Mag Hill, the JLD showing, the Terra mine, and the Dennis showing from the Great Bear magmatic zone (Northwest Territories, Canada) are examined. Dark irregular zones observed under scanning electron microscope backscattered images have lower REE contents when measured using electron probe microanalyzer and/or laser ablation inductively coupled plasma mass spectrometry. REE remobilization and precipitation of secondary allanite and monazite during metasomatic alteration of the fluorapatite is inferred based on petrographic evidence and dissolution pits in the REE-depleted zones of the fluorapatite. Allanite is the most common secondary REE-rich phase and can be explained by the predominance of calcic alteration during the low-temperature alteration. Fluorapatite grains with Mn content above 500 ppm and where LREE leaching occurred have green or green to yellow cathodoluminescence responses. Single grains of fluorapatite also record an atypical decoupling of U and Th interpreted to be caused by potassic-ferric/ferrous alteration. This metasomatism leads to fluorapatite grains with localized increases in Th content near fractures and edges (e.g., from ∼50 to ∼1000 ppm). The identification of these textural characteristics, geochemical signatures, and cathodoluminescence responses in fluorapatite from the systems covered by this study is a significant first step in the development of an indicator mineral exploration method for prospecting for IOA and IOCG deposits in the Great Bear magmatic zone and beyond.