Banded iron formation (BIF)-hosted iron ore deposits in the Windarling Range are located in the lower greenstone succession of the Marda–Diemals greenstone belt, Southern Cross domain, Yilgarn Craton and constitute a total hematite–martite–goethite ore resource of minimum 52 Mt at 60 wt.% Fe (0.07 P). Banded iron formation is interlayered with high-Mg basalts at Windarling and precipitated during episodes of volcanic quiescence. Trace element content and the rare earth element (REE) ratios Y/Ho (42 to 45), Sm/Yb (1.5), together with positive La and Gd anomalies in ‘least-altered’ hematite–magnetite–metachert–BIF indicate the precipitation from Archean seawater that was fertilised by hydrothermal vent fluids with a basaltic HREE-Y signature. Hypogene iron ore in sub-greenschist facies metamorphosed BIF formed during three distinct stages: ore stage 1 was a syn- to post-metamorphic, syn-D1, Fe–Ca–Mg–Ni–Co–P–REE metasomatism that produced local Ni–REE-rich Fe–dolomite–magnetite alteration in BIF. Hydrothermal alteration was induced by hot fluid flow controlled by brittle–ductile reactivation of BIF-basalt margins and crosscutting D1 faults. The Ni–Co-rich content of dolomite and a shift in REE ratios in carbonate-altered BIF towards Archean mafic rock signature (Y/Ho to 31 to 40, Sm/Yb to 1 to 2 and Gd/Gd* to 1.2 to 1.4) suggest that high-Mg basalts in the Windarling Range were the primary source of introduced metals. During ore stage 2, a syn-deformational and likely acidic and oxidised fluid flow along BIF-basalt margins and within D1 faults leached carbonate and precipitated lepidoblastic and anhedral/granoblastic hematite. High-grade magnetite–hematite ore is formed during this stage. Ore stage 3 hydrothermal specular hematite (spcH)–Fe–dolomite–quartz alteration was controlled by a late-orogenic, brittle, compressional/transpressional stage (D4; the regional-scale shear-zone-related D3 is not preserved in Windarling). This minor event remobilised iron oxides, carbonate and quartz to form veins and breccia but did not generate significant volumes of iron ore. Ore stage 4 involved Mesozoic(?) to recent supergene oxidation and hydration in a weathering environment reaching down to depths of ∼100 to maximum 200 m below surface. Supergene ore formation involved goethite replacement of dolomite and quartz as well as martitisation. Important ‘ground preparation’ for supergene modification and upgrade were mainly the formation of steep D1 to D4 structures, steep BIF/basalt margins and particularly the syn-D1 to syn-D2 carbonate alteration of BIF that is most susceptible to supergene dissolution. The Windarling deposits are structurally controlled, supergene-modified hydrothermal iron ore systems that share comparable physical, chemical and ore-forming characteristics to other iron ore deposits in the Yilgarn Craton (e.g. Koolyanobbing, Beebyn in the Weld Range, Mt. Gibson). However, the remarkable variety in pre-, syn- and post-deformational ore textures (relative to D1 and D2) has not been described elsewhere in the Yilgarn and are similar to the ore deposits in high-strain zones, such as of Brazil (Quadrilatero Ferrifero or Iron Quadrangle) and Nigeria. The overall similarity of alteration stages, i.e. the sequence of hydrothermal carbonate introduction and hypogene leaching, with other greenstone belt-hosted iron ore deposits supports the interpretation that syn-orogenic BIF alteration and upgrade was crucial in the formation of hypogene–supergene iron ore deposits in the Yilgarn Craton and possibly in other Archean/Paleoproterozoic greenstone belt settings worldwide.