Molybdenum (Mo) and its isotopes have been used to retrieve palaeoenvironmental information on the ocean-atmosphere system through geological time. Their application has so far been restricted to rocks least affected by severe metamorphism and deformation, which may erase or alter palaeoenvironmental signals. Environmental Mo-isotope signatures can be retrieved if the more manganese (Mn)-enriched rocks are isotopically depleted and the maximum range of δ98Mo values is close to the ~2.7‰ Mo-isotope fractionation known from Mo sorption onto Mn oxides at low temperature. Here, we show that the Morro da Mina Mn-ore deposit in Minas Gerais, Brazil, contains Mn-silicate-carbonate ore and associated graphitic schist that likely preserve δ98Mo of Palaeoproterozoic seawater, despite a metamorphic overprint of at least 600 °C. The extent of Mo-isotope fractionation between the Mn-silicate-carbonate ore and the graphitic schist is similar to modern Mn-oxide precipitates and seawater. Differences in δ98Mo signals are broadly reflected in cerium (Ce) anomalies, which suggest an oxic-anoxic-stratified Palaeoproterozoic ocean.