The early ocean was characterized by anoxic, iron-rich (ferruginous) conditions before the rise of atmospheric oxygen ∼2.45 b.y. ago. A proxy for ferruginous conditions in the ancient ocean is the deposition of banded iron formations (BIFs), which are iron- and silica-rich chemical sediments whose constituents were largely derived from seawater. Although experiments simulating ancient ocean chemistry support the rapid growth of iron-silicate phases, the main iron precipitates are hypothesized to have been ferric oxyhydroxides. The paradox between the prevailing reducing conditions and the deposition of oxidized iron phases is explained by biologically mediated oxidation in the water column. New high-resolution microscopy of BIFs and shales throughout the 2.63–2.45 b.y. old Hamersley Group, Australia, reveals the presence of vast quantities of nanometer-sized iron-silicate particles in laminated chert. The nanoparticles are finely disseminated in early diagenetic chert and locally define sedimentary lamination, indicating that they represent relicts of the original sediments. By inference from experimental studies simulating the composition of the early Precambrian ocean, we suggest that the nanoparticles precipitated from anoxic seawater enriched in silica and dissolved iron, and were silicified upon deposition. The prevalence of iron-silicate nanoparticles implies that they were pervasive background precipitates in ferruginous, silica-enriched oceans, forming the primary sediments of BIFs during periods of enhanced submarine mafic volcanism. Our results imply that silicate precipitation was a major sink of seawater iron and silica before the Great Oxidation Event and, because of the reactivity of nanoparticle surfaces, may also have influenced the transport and geochemical cycling of trace metals and nutrients. Our hypothesis that the basic building blocks of BIFs were predominantly iron-silicate muds rather than iron oxides and/or hydroxides may lead to new insights into seawater chemistry on the early Earth and the role of biology in the deposition of BIFs.