Ocean dynamics in the equatorial Pacific drive tropical climate patterns that affect marine and terrestrial ecosystems worldwide. How this region will respond to global warming has profound implications for global climate, economic stability and ecosystem health. As a result, numerous studies have investigated equatorial Pacific dynamics during the Pliocene (5.3-2.6 million years ago) and late Miocene (around 6 million years ago) as an analogue for the future behaviour of the region under global warming. Palaeoceanographic records from this time present an apparent paradox with proxy evidence of a reduced east-west sea surface temperature gradient along the equatorial Pacific-indicative of reduced wind-driven upwelling-conflicting with evidence of enhanced biological productivity in the east Pacific that typically results from stronger upwelling. Here we reconcile these observations by providing new evidence for a radically different-from-modern circulation regime in the early Pliocene/late Miocene that results in older, more acidic and more nutrient-rich water reaching the equatorial Pacific. These results provide a mechanism for enhanced productivity in the early Pliocene/late Miocene east Pacific even in the presence of weaker wind-driven upwelling. Our findings shed new light on equatorial Pacific dynamics and help to constrain the potential changes they will undergo in the near future, given that the Earth is expected to reach Pliocene-like levels of warming in the next century.