The Madeira deposit is a world-class tin (Sn) deposit characterized by a unique mineralogical assemblage composed of a massive cryolite (NaAlF3) deposit associated with economically important metals like Nb (0.20 wt% Nb2O5). Although hydrothermal alteration has long been recognized in the cryolite formation, its effects on the mineralization and mobility of Nb remain obscure. This study presents new data on the Nb mineralization of the Pitinga core and border albite-enriched granites provided by nanoscale and site-selective approaches, using transmission electron microscopy and synchrotron-radiation analyses. Pyrochlore is the main Nb ore mineral with three distinct compositional types (U-Pb, Pb-U and Y-bearing varieties). Hydrothermal processes lead to the extensive alteration of pyrochlore into columbite (later designated as columbitization) by a coupled dissolution-reprecipitation mechanism, which evidences the alterability of pyrochlore in a hydrothermal context. Nanoscale analyses of veins and reaction interfaces reveal the presence of additional Nb hosts including fergusonite-(Y), Nb-bearing uraninite and Nb-bearing coffinite which formed from the alteration of pyrochlore. The nature of the altered phases mainly depends on the composition of the parent pyrochlore. Their formation, occurring in absence of direct proximity with remaining pyrochlore, shows that Nb mobilization at macroscopic scale is possible in F-rich reducing fluids. Niobium L3-edge XANES spectroscopy on bulk samples representative of the different facies show that hydrothermal processes change the Nb mineralization by converting primary U-Pb-bearing pyrochlore into columbite and Pb-U/Y-bearing pyrochlores. The columbitization process of pyrochlore led to the increase of the Nb ore grade. Nonetheless, hydrothermal alteration modified Nb mineral liberation, thereby limiting the recovery of the full range of Nb host phases.