Precambrian banded iron formations provide an extensive archive of pivotal environmental changes and the evolution of biological processes on early Earth. The formations are characterized by bands ranging from micrometre- to metre-scale layers of alternating iron- and silica-rich minerals. However, the nature of the mechanisms of layer formation is unknown. To properly evaluate this archive, the physical, chemical and/or biological triggers for the deposition of both the iron- and silica-rich layers, and crucially their alternate banding, must be identified. Here we use laboratory experiments and geochemical modelling to study the potential for a microbial mechanism in the formation of alternating iron–silica bands. We find that the rate of biogenic iron(III) mineral formation by iron-oxidizing microbes reaches a maximum between 20 and 25 °C. Decreasing or increasing water temperatures slow microbial iron mineral formation while promoting abiotic silica precipitation. We suggest that natural fluctuations in the temperature of the ocean photic zone during the period when banded iron formations were deposited could have led to the primary layering observed in these formations by successive cycles of microbially catalysed iron(III) mineral deposition and abiotic silica precipitation.