An Early Quaternary shallow submarine hydrothermal iron formation (IF) in the Cape Vani sedimentary basin (CVSB) on Milos Island, Greece, displays banded rhythmicity similar to Precambrian banded iron formation (BIF). Sedimentary, stratigraphic reconstruction, biogeochemical analysis and micro-nanoscale mineralogical characterization confirms the Milos rocks as modern Precambrian BIF analogues. Spatial coverage of the BIF-type rocks in relation to the economic grade Mn ore that brought prominence to the CVSB implicates tectonic activity and changing redox in the deposition of the BIF-type rocks. Field-wide stratigraphic and biogeochemical reconstruction demonstrates two temporal and spatially isolated iron deposits in the CVSB with distinct sedimentological character. Petrographic screening suggest the previously described photoferrotrophic-like microfossil-rich IF (MFIF), accumulated on basement andesite in a ~ 150 m wide basin, in the SW margin of the basin. A strongly banded non-fossiliferous IF (NFIF) caps the Mn-rich sandstones at the transition to the renowned Mn-rich formation. Geochemical evidence relates the origin of the NFIF to periodic submarine volcanism and water column oxidation of released Fe(II) in conditions apparently predominated by anoxia, similar to the MFIF. This is manifested in the lack of shale-normalized Ce anomalies. Raman spectroscopy pairs hematite-rich grains in the NFIF with relics of a carbonaceous material carrying an average δ 13 C org signature of ~ −25 ‰. However, a similar δ 13 C org signature in the MFIF is not directly coupled to hematite by mineralogy. The NFIF, which post dates large-scale Mn deposition in the CVSB, is composed primarily of amorphous Si (opal-SiO 2 · nH 2 O) while crystalline quartz (SiO 2 ) predominates the MFIF. An intricate interaction between tectonic processes, changing redox, biological activity and abiotic Si precipitation, formed the unmetamorphosed BIF-type deposits.