The redox chemistry of anoxic continental margin settings evolved from widespread sulfide-containing (euxinic) conditions to a global ferruginous (iron-containing) state in the early Neoproterozoic era (from similar to 1 to 0.8 billion years ago). Ocean redox chemistry exerts a strong control on the biogeochemical cycling of phosphorus, a limiting nutrient, and hence on primary production, but the response of the phosphorus cycle to this major ocean redox transition has not been investigated. Here, we use a geochemical speciation technique to investigate the phase partitioning of phosphorus in an open marine, early Neoproterozoic succession from the Huainan Basin, North China. We find that effective removal of bioavailable phosphorus in association with iron minerals in a globally ferruginous ocean resulted in oligotrophic (nutrient limited) conditions, and hence a probable global decrease in primary production, organic carbon burial and, subsequently, oxygen production. Nevertheless, phosphorus availability and organic carbon burial were sufficient to maintain an oxidizing atmosphere. These data imply substantial nutrient-driven variability in atmospheric oxygen levels through the Proterozoic, rather than the stable levels commonly invoked. Early Neoproterozoic marine productivity fell due to nutrient drawdown following a switch from an iron-rich to a sulfide-rich ocean, according to records of phosphorus geochemistry measured from sedimentary sections in North China.