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Diagenesis is a double-edged sword of geochemical recordings. It makes us always doubt about the representativeness of many geochemical indicators, especially the isotope and mineral related. It also provides a window to explore the biogeochemical processes at the water–rock interface, which are related to the interactions between the hydrosphere, biosphere, and lithosphere. In this study, we identified microbial early diagenesis in lacustrine ostracods from the Songliao Basin 91.35 million years ago by using in situ mineralogical and carbon isotope analytical methods. Our results suggest multiple biological early-diagenesis processes and the formation of a ferric and methane transition zone (FMTZ) in the sulfate-poor pore water, which are conducive to the formation of dolomite and ankerite. These secondary carbonate minerals related to dissimilatory iron reduction and methanogenesis have heavier carbon isotopic compositions than the calcified ostracod shell in the water column and might bring interferences to the geochemical parameters of ostracods. [ABSTRACT FROM AUTHOR]