Mesoarchean Algoma-type BIF in the Yilgarn Craton are locally enriched by secondary processes to iron concentrations approaching 72 wt% Fe. While their near-surface goethite–hematite ores are unequivocally the product of supergene fluid alteration, their deeper magnetite and crystalline hematite–martite ores have a contentious origin. This study shows that magnetite ores formed after diagenesis and peak greenschist facies metamorphism of BIF, coinciding with regional deformation events. The ores formed by a multi-stage process involving initial replacement of primary quartz bands in BIF by hypogene carbonate minerals, followed by the dissolution of the carbonate and concentration of magnetite. At the Beebyn deposit, the earliest fluids were hot (~440 °C), CO2–vapor-rich, and were likely derived from felsic magmatic fluids. In contrast, the fluids responsible for carbonate alteration at the Matthew Ridge, Koolyanobbing, and Windarling deposits were cooler (366–125 °C) and aqueous-rich with salinities from 0.3 to 43.9 wt% NaCl equiv. Their Cl–Br and C–O isotopic ratios suggest they are the product of mixing between magmatic fluids and heated seawater. In all deposits, later cooling (~178–98 °C) of these fluids led to dissolution of carbonate minerals and concentration of magnetite. Dated monazite and xenotime from magnetite ores demonstrates that fluid alteration of BIF began in the Mesoarchean and continued episodically through to the Paleoproterozoic. Later specular hematite-rich veins that cut and modify magnetite ores crystallized from aqueous-rich fluids that are more oxidized, with salinities from 0 to 28.7 wt% NaCl equiv. and crystallization temperatures of 243–85 °C. Their Cl–Br and C–O isotopic fluid ratios indicate that they formed from mixing between heated seawater and meteoric waters. The BIF-hosted iron deposits in the Yilgarn Craton show remarkable similarities with the well-studied iron deposits in the Carajás Mineral Province and Hamersley Basin. They all show the same transition through time from magnetite- to hematite-rich ores. Subsequent episodic, tectonically-driven, fluid alteration events led to further iron enrichment in these deposits. The transition in ore types most likely corresponds to a common guiding process, namely the uplift of crustal rocks containing BIF – resulting in the progressive shallowing of fluid alteration pathways and the greater influence of cooler, more oxidized, hydrothermal fluids. Unlike iron deposits hosted by Algoma-type BIF in the Yilgarn and Carajás, iron deposits hosted by Superior-type BIF in the Hamersley Basin display a greater influence of oxidized marine and meteoric waters, without involvement of magmatic fluids.