Multiple generations of magnetite are common in many magmatic-hydrothermal Fe deposits, which can be formed by different mechanisms. This study investigates magnetite from the Alemao IOCG deposit (Brazil) characterized by inclusion-rich cores (Mag-1) and inclusion-poor rims (Mag-2), using electron probe microanalyzer and high-resolution transmission electron microscopy (HRTEM), to understand its formation mechanism and implications for Fe and Cu mineralization. Electron probe microanalysis shows that Mag-1 has Si and Mg contents of 0.28–1.15 wt% and 0.11–0.49 wt%, respectively, higher than Mag-2. Mineral nanoinclusions of minnesotaite, chlorite, quartz, and minor Ti-rich magnetite in the Mag-1 account for the relatively high Si and Mg in the Mag-1, as measured by electron probe microanalysis. The crystal orientation of nanoinclusions relative to the host Mag1 indicates formation by growth entrapment, where they crystallized from boundary layer supersaturated fluids under non-equilibrium conditions.Identification of a reaction front, spatial coupling of parent and product phases at micro- and nano-meter scales support the formation of Alemao Mag2 by coupled dissolution and reprecipitation (CDR). Variations in fluid composition rather than fluctuations in conditions such as temperature and oxygen fugacity are the factors inducing CDR. A conceptual model is proposed for the formation of Alemao magnetite where Fe-rich fluids formed inclusion-rich primary magnetite and CDR reactions modified the texture and chemical composition of primary magnetite to form a core rich, and a rim poor, in nanoinclusions. During CDR, impurities of Si, Ca, Al, Mn, and Mg and nanoinclusions are removed from the primary magnetite and formed product magnetite with higher Fe. The progressive enrichment of Cu from Mag-1 to Mag-2 during CDR indicates that a Cu-rich fluid related to the Cu-Au mineralization is responsible the formation of Cu-rich Mag-2 and chalcopyrite. Therefore, micron- to nano-scale characterization of magnetite with multiple generations can provide important constraints on fluid evolution in ore system.