Ferruginous conditions prevailed in the oceans through much of Earth's history. However, minerals recording these conditions remain difficult to interpret in terms of biogeochemical processes prior to lithification. In Lake Towuti, Indonesia, ferruginous sediments are deposited under anoxic sulfate-poor conditions similar to the Proterozoic oceans, allowing the study of mineralogical (trans)formations during microbial diagenesis. Comprehensive pore water geochemistry, high resolution geochemical core profiles, and electron microscopy of authigenic minerals revealed in situ formation of magnetite, millerite, and abundant siderite and vivianite along a 100 m long sequence. Framboidal magnetites represent primary pelagic precipitates, whereas millerite, a sulfide mineral often overlooked under sulfate-poor conditions, shows acicular aggregates entangled with siderite and vivianite resulting from saturated pore waters and continuous growth during burial. These phases act as biosignatures of microbial iron and sulfate reduction, fermentation and methanogenesis, processes clearly traceable in pore water profiles. Variability in metal and organic substrates attests to environment driven processes, differentially sustaining microbial processes along the stratigraphy. Geochemical profiles resulting from microbial activity over 200 kyr after deposition provide constraints on the depth and age of mineral formation within ferruginous records
