The silicon (Si) cycle is intimately interlinked with other biogeochemical cycles (e.g., carbon and nitrogen) and plays an important role in regulating long-term global climate change and biotic evolution in Earth's history. The abundance of cherts in Mesoproterozoic shallow-marine carbonates implies unique environmental conditions for silica precipitation, but the driving mechanism behind the Si cycle in Mesoproterozoic oceans remains unclear. In this paper, we report an integrated study of the cherts from the ∼1.48 Ga Wumishan Formation of North China. The Wumishan cherts predominantly consist of microquartz (∼90%), with some silica-replaced carbonate (∼5%) and minor pyrite (∼1%) grains, indicating that the cherts were largely formed through primary silica precipitation. High germanium/silicon molar ratios (Ge/Si = 0.71–19.1 μmol/mol; mean = 8.83) and positive europium anomalies (Eu/Eu* = 0.41–2.42; mean = 1.41) of the cherts suggest a considerable contribution from hydrothermally derived Si. Diverse microbial components, including organic-rich filaments, EPS (extracellular polymeric substances) relics, mat fragments and picocyanobacteria fossils, are observed in the Wumishan cherts. These components, together with abundant organominerals resulted from the interactions of microbes and dSi in ambient environments, imply that microbial activities played critical roles in silica deposition. The Si liberated from degraded EPS or EPS-Si complex may have locally increased the dSi concentrations and changed chemical conditions in the substrate and pore-waters, promoting silica precipitation. Given that picocyanobacteria and some other prokaryotes can accumulate significant amounts of silica in their cells and EPS, biogenic silica from decomposed microbial biomass may have exerted an important influence on silica precipitation in shallow-marine environments of the Mesoproterozoic ocean.