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Abstract Whether Mn carbonates can be used as a proxy for the oxygenation event is debated. Here we examined the Early Cretaceous lacustrine Mn carbonates from North China, which contain abundant microbial fossils. The extremely positive δ13C (up to +15‰ relative to Vienna Peedee belemnite) and micro‐area enrichment of Ni strongly indicate a methanogenic archaea origin of these microorganisms. Transmission electron microscope and electron energy loss spectroscopy show the nanoscale transformation of Mn‐oxides (Mg‐exchanged phyllomanganate) to Mn carbonates (kutnohorite), on extracellular polymeric substances. The reaction of the Mn oxides with organic matter resulted in increasing pH and alkalinity, together with the fluctuating pH, offering a suitable micro‐environment for the transformation processes. These Mn carbonates are therefore indicative of an oxidized, sulfate‐absent environment. The depicted scenario serves as a reference to ocean of the early Earth and provides a referable Mn oxide tracer for determining the emergence of the Great Oxidation Event.