<p>Carbonatites and phoscorites are the world’s main sources of REE and Nb, yet their genetic relationship remains controversial. In the Alto Paranaíba Igneous Province (APIP) of central Brazil—the world’s largest producer of Nb—the Boa Vista Nb deposit exploits residual soils from pyrochlore-rich phoscorites associated with carbonatites. Assessing petrogenetic processes in the Boa Vista deposit is challenging due to the intense alteration of the host rocks, including CO₂-, K- and OH⁻-rich alteration/fenitization, which obscures bulk geochemical signals and hinder reconstruction of magmatic processes. Here, we integrate field observations from the Boa Vista mine with µ-XRF mineral mapping, EMPA data and LA-ICP-MS trace element analysis of magnetite to investigate the petrogenetic relationship between carbonatites and phoscorites. Macrotextural evidence from drill cores reveals rhythmic intercalation of carbonatite and phoscorite cumulate layers at depths exceeding 500&#xa0;m. Magnetite from both rock types exhibits subhedral habits with ilmenite lamellae oxy-exsolutions without martitization, indicating high-temperature magmatic crystallization from a parental carbonatite magma. Phoscorite magnetite shows enrichment in HFSE relative to those in carbonatites, a signature consistent with co-crystallization of pyrochlore group minerals. In particular, Nb contents in magnetite are an order of magnitude higher in high-grade Nb deposits like Boa Vista compared to low-grade occurrences worldwide, suggesting its potential as a grade indicator. These results suggest that phoscorites may form through efficient heavy crystal segregation during early carbonatite fractionation, rather than from a specific immiscible phoscorite magma. This research contributes to our understanding of high-grade Nb ores in alkaline-carbonatite complexes, highlighting crystal/magma segregation as a crucial mechanism for forming Nb-rich phoscorites.</p>