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The El Niño Southern Oscillation (ENSO) is highly dependent on coupled atmosphere-ocean interactions and feedbacks, suggesting a tight relationship between ENSO strength and background climate conditions. However, the extent to which background climate state determines ENSO behavior remains in question. Here we present reconstructions of total variability and El Niño amplitude from individual foraminifera distributions at discrete time intervals over the past ~285,000 years across varying atmospheric CO₂levels, global ice volume and sea level, and orbital insolation forcing. Our results show a strong correlation between eastern tropical Pacific Ocean mixed-layer thickness and both El Niño amplitude and central Pacific variability. This ENSO-thermocline relationship implicates upwelling feedbacks as the major factor controlling ENSO strength on millennial time scales. The primacy of the upwelling feedback in shaping ENSO behavior across many different background states suggests accurate quantification and modeling of this feedback is essential for predicting ENSO’s behavior under future climate conditions.