Variations in ocean productivity are driven largely by nutrient supply to the photic zone, but temporal records of nutrient variability are sparse. Here we show scleractinian coral P/Ca proxy records of variations in phosphate concentrations during El Niño Southern Oscillation (ENSO) cycles in the central equatorial Pacific. Covarying P/Ca records in Porites corals from Christmas and Fanning Islands show a regional ~40% decrease during the upwelling relaxation of the 1997–1998 El Niño, consistent with less frequent nutrient measurements from this area. Similar ~35–45% skeletal P/Ca decreases occur during the 1982–1983 and 1986–1987 El Niño events, which predate satellite color and regional nutrient measurements. After each El Niño event, nutrient increases lag temperature recovery by 4–12 months, likely reflecting uptake by massive phytoplankton blooms that followed resumption of upwelling. The results support the utility of coral P/Ca to probe the mechanisms linking ENSO, equatorial upwelling, and carbon cycling in the past.