The Matongo carbonatite intrusive body in the Neoproterozoic Upper Ruvubu alkaline plutonic complex (URAPC) in Burundi is overlain by an economic phosphate ore deposit that is present as breccia lenses. The ore exhibits evidence of supergene enrichment but also preserves textures related to the concentration of fluorapatite in the carbonatitic system. Magmatic fluorapatite is abundant in the ore and commonly occurs as millimeter-sized aggregates. It is enriched in light rare earth elements (LREE), which is especially apparent in the final generation of magmatic fluorapatite (up to 1.32 wt% LREE2O3). After an episode of metasomatism (fenitization), which led to the formation of K-feldspar and albite, the fluorapatite-rich rocks were partly brecciated. Oxygen and carbon isotope compositions obtained on the calcite forming the breccia matrix (δ18O = 22.1 ‰ and δ13C = −1.5 ‰) are consistent with the involvement of a fluid resulting from the mixing of magmatic-derived fluids with a metamorphic fluid originating from the country rocks. In a subsequent postmagmatic event, the carbonates hosting fluorapatite were dissolved, leading to intense brecciation of the fluorapatite-rich rocks. Secondary carbonate-fluorapatite (less enriched in LREE with 0.07–0.24 wt% LREE2O3 but locally associated with monazite) and coeval siderite constitute the matrix of these breccias. Siderite has δ18O values between 25.4 and 27.7 ‰ and very low δ13C values (from −12.4 to −9.2 ‰), which are consistent with the contribution of organic-derived low δ13C carbon from groundwater. These signatures emphasize supergene alteration. Finally, the remaining voids were filled with a LREE-poor fibrous fluorapatite (0.01 wt% LREE2O3), forming hardened phosphorite, still under supergene conditions. Pyrochlore and vanadiferous magnetite are other minerals accumulated in the eluvial horizons. As a consequence of the supergene processes and fluorapatite accumulation, the phosphate ore, which contains 0.72 to 38.01 wt% P2O5, is also enriched in LREE (LaN/YbN from 47.1 to 83.5; ΣREE between 165 and 5486 ppm), Nb (up to 656 ppm), and V (up to 1232 ppm). In the case of phosphate exploitation at Matongo, REE could prove to have a subeconomic potential to be exploited as by-products of phosphates.