Abstract Magnetofossils, produced by magnetotactic bacteria, are widespread in marine sediments and are thought to be linked to oxygen concentrations. Until recently, their applications as a quantitative proxy for bottom water oxygen (BWO) are limited due to the lack of data from modern marine environments. Here, we present a multi‐basin calibration of magnetofossil assemblages from a broad range of BWO concentrations using a large set of surface sediments. We find that both coercivity fractions and crystal morphologies of magnetofossils are linearly correlated with BWO over ∼0–230 μmol/kg. We also find that while organic carbon contents primarily control magnetofossil abundance, it only has a weak influence on magnetofossil morphologies compared to BWO. Our calibration establishes magnetofossils as a quantitative oxygenation proxy, which provides rapid, and high‐resolution reconstructions of past ocean oxygenation and associated deep‐ocean carbon storage under climate transitions.