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 Nino-Southern Oscillation (ENSO) activity, and the tropical Pacific zonal gradient for the past millennium from Galapagos 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 Nina pattern.