Estimates of early atmosphere compositions from metamorphosed banded iron formations (BIFs) including the well-studied ≥3.7 BIFs of the Isua supracrustal belt (Greenland) are dependent on knowledge of primary versus secondary Fe-mineralogical assemblages. Using new observations from locally well preserved domains, we interpret that a previously assumed primary redox indicator mineral, magnetite, is secondary after sedimentary Fe-clays (probably greenalite) ± carbonates. Within ∼3.7 Ga Isua BIF, pre-tectonic nodules of quartz + Fe-rich amphibole ± calcite reside in a fine-grained (≤100 μm) quartz + magnetite matrix. We interpret the Isua nodule amphibole as the metamorphosed equivalent of primary Fe-rich clays, armoured from diagenetic oxidative reactions by early silica concretion. Additionally, in another low strain lacunae, ∼3.76 Ga BIF layering is not solid magnetite but instead fine-grained magnetite + quartz aggregates. These magnetite + quartz aggregates are interpreted as the metamorphosed equivalent of Fe-clay-rich layers that were oxidised during diagenesis, because they were not armoured by early silicification. In almost all Isua BIF exposures, this evidence has been destroyed by strong ductile deformation. The Fe-clays likely formed by abiotic reactions between aqueous Fe2+ and silica. These clays along with silica ± carbonate were deposited below an oceanic Fe-chemocline as the sedimentary precursors of BIF. Breakdown of the clays on the sea floor may have been by anaerobic oxidation of Fe2+, a mechanism compatible with iron isotopic data previously published on these rocks. The new determinations of the primary redox-sensitive Fe-mineralogy of BIF significantly revise estimates of early Earth atmospheric oxygen and CO2 content, with formation of protolith Fe-rich clays and carbonates compatible with an anoxic Eoarchean atmosphere with much higher CO2 levels than previously estimated for Isua and in the present-day atmosphere.