Description: Upwelling ocean currents associated with oxygen minimum zones (OMZs) supply nutrients fuelling intense marine productivity. Perturbations in the extent and intensity of OMZs are projected in the future, but it is currently uncertain how this will impact fluxes of redox‐sensitive trace metal micronutrients to the surface ocean. Here we report seawater concentrations of Fe, Mn, Co, Cd, and Ni alongside the redox indicator iodide/iodate in the Peruvian OMZ during the 2015 El Niño event. The El Niño drove atypical upwelling of oxygen‐enriched water over the Peruvian Shelf, resulting in oxidized iodine and strongly depleted Fe (II), total dissolved Fe, and reactive particulate Fe concentrations relative to non‐El Niño conditions. Observations of Fe were matched by the redox‐sensitive micronutrients Co and Mn, but not by non‐redox‐sensitive Cd and Ni. These observations demonstrate that oxygenation of OMZs significantly reduces water column inventories of redox‐sensitive micronutrients, with potential impacts on ocean productivity. Plain Language Summary Some trace metals, including iron, are essential micronutrients for phytoplankton growth. However, the solubility of iron is very low under oxygenated conditions. Consequently, restricted iron availability in oxygen‐rich seawater can limit phytoplankton growth in the ocean, including in the Eastern Tropical South Pacific. Under typical conditions, depleted oxygen on the South American continental shelf is generally thought to enhance iron supply to the ocean, fuelling phytoplankton productivity in overlying waters. However, the impact of changes in oxygenation, which are predicted to occur in the future, are not known. The 2015 El Niño event led to unusually high oxygen on the Peruvian shelf, offering a system‐scale test on how oxygen influences seawater iron concentrations. We show that El Niño‐driven oxygenation resulted in marked decreases in iron and other metals sensitive to oxygen (cobalt and manganese), whilst metals not sensitive to oxygen (cadmium and nickel) were unaffected. The measured reductions in iron may have led to decreased phytoplankton productivity.