Tropical Pacific Ocean dynamics during the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA) are poorly characterized due to a lack of evidence from the eastern equatorial Pacific. We reconstructed sea surface temperature, El Niño–Southern Oscillation (ENSO) activity, and the tropical Pacific zonal gradient for the past millennium from Galápagos ocean sediments. We document a mid-millennium shift (MMS) in ocean-atmosphere circulation around 1500–1650 CE, from a state with dampened ENSO and strong zonal gradient to one with amplified ENSO and weak gradient. The MMS coincided with the deepest LIA cooling and was probably caused by a southward shift of the intertropical convergence zone. The peak of the MCA (900–1150 CE) was a warm period in the eastern Pacific, contradicting the paradigm of a persistent La Niña pattern.