Understanding microbial mediation in sediment-hosted Mn deposition has gained importance in low-temperature ore genesis research. Here we report Mn oxide ores dominated by todorokite, vernadite, hollandite, and manjiroite, which cement Quaternary microbially induced sedimentary structures (MISS) developed along bedding planes of shallow-marine to tidal-flat volcaniclastic sandstones/sandy tuffs, Cape Vani paleo-hydrothermal vent field, Milos, Greece. This work aims to decipher the link between biological Mn oxide formation, low-T hydrothermalism, and, growth and preservation of Mn-bearing MISS (MnMISS). Geobiological processes, identified by microtexture petrography, scanning and transmission electron microscopy, lipid biomarkers, bulk- and lipid-specific δ¹³C_organic composition, and field data, and, low-temperature hydrothermal venting of aqueous Mn²⁺ in sunlit shallow waters, cooperatively enabled microbially-mediated Mn (II) oxidation and biomineralization. The MnMISS biomarker content and δ¹³C_org signatures strongly resemble those of modern Mn-rich hydrothermal sediments, Milos coast. Biogenic and syngenetic Mn oxide precipitation established by electron paramagnetic resonance (EPR) spectroscopy and petrography, combined with hydrothermal fluid flow-induced pre-burial curing/diagenesis, may account for today’s crystalline Mn oxide resource. Our data suggests that MISS are not unique to cyanobacteria mats. Furthermore, microbial mats inhabited by aerobic methanotrophs may have contributed significantly to the formation of the MnMISS, thus widening the spectrum of environments responsible for marine Mn biometallogenesis.