The Datangpo Formation manganese deposits (DFMnD) in South China formed during the interglacial stage between the Sturtian and Marinoan glaciations of the Cryogenian period. These black shale-hosted deposits are composed of massive Mncarbonates with microscopic laminae/laminations and cherty veins. To date, it has been thought that the DFMnD formed through inorganic processes, which were controlled by redox changes in the post-Sturtian Nanhua Rift Basin, South China. However, in this study, systematic petrographic, mineralogical, and geochemical analyses indicate a microbially mediated origin of the Mn ore deposits. Mineralized microbial woven micro-textures (observed at the μm scale) and microbial fossils are common in the laminated Mn-carbonate ores. We infer that microbial enzyme activity formed poorly crystallized Mn oxide/hydroxides and carbonaceous material, which 2 transformed to rhodochrosite, kutnohorite, ankerite/dolomite, framboidal pyrite, and apatite via diagenesis. Some micro-scale quartz and K-feldspar may be detrital but most appears to have formed during diagenesis or through hydrothermal activity. A micro-mineralogical profile determined by 2500 spectra via high-resolution in situ micro-Raman spectroscopy also revealed cyclic laminations of Ca-rhodochrosite as microbialite (ankerite/dolomite) and quartz, indicating a mineralized biomat system. Ca-rhodochrosite transformed to kutnohorite under elevated temperatures, as indicated by the maturation level of organic matter (determined via Raman spectroscopy). Alternating micro-laminae denote cyclic changes in microbial groups (Mn-and Fe-oxidizing microbes versus cyanobacteria) during the formation of the Mn ore deposits. Our proposed model for the microbially mediated metallogenesis of Mn-carbonate deposits begins with enzymatic multi-copper oxidase processes associated with autotrophic microbial activity under obligatory oxic conditions, which results in the precipitation of Mn bio-oxides. Following their burial in organic-rich sediments, the Mn(IV) oxides and hydroxides are reduced, producing soluble Mn(II) via processes mediated by heterotrophic microbes under suboxic conditions, which in turn form the Mn-carbonates. This microbial metallogenesis model for the Cryogenian DFMnD in South China is similar to that proposed for the Jurassic Úrkút Mn deposit in Hungary, indicating that a two-step microbially mediated process of Mn ore formation might be common throughout geological history.