AbstractOcean chlorophyll concentration, a proxy for phytoplankton, is strongly influenced by internal ocean dynamics such as those associated with El Niño–Southern Oscillation (ENSO). Observations show that ocean chlorophyll responses to ENSO generally lead sea surface temperature (SST) responses in the equatorial Pacific. A long‐term global Earth system model simulation incorporating marine biogeochemical processes also exhibits a preceding chlorophyll response. In contrast to simulated SST anomalies, which significantly lag the wind‐driven subsurface heat response to ENSO, chlorophyll anomalies respond rapidly. Iron was found to be the key factor connecting the simulated surface chlorophyll anomalies to the subsurface ocean response. Westerly wind bursts decrease central Pacific chlorophyll by reducing iron supply through wind‐driven thermocline deepening but increase western Pacific chlorophyll by enhancing the influx of coastal iron from the maritime continent. Our results mechanistically support the potential for chlorophyll‐based indices to inform seasonal ENSO forecasts beyond previously identified SST‐based indices.