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Fully and accurately reconstructing changes in oceanic productivity and carbon export and their controls is critical to determining the efficiency of the biological pump and its role in the global carbon cycle through time, particularly in modern CO₂source regions like the eastern equatorial Pacific (EEP). Here we present new high-resolution records of sedimentary²³⁰Th-normalized opal and nannofossil carbonate fluxes and [²³¹Pa/²³⁰Th]xs ratios from site MV1014-02-17JC in the Panama Basin. We find that, across the last deglaciation, phytoplankton community structure is driven by changing patterns of nutrient (nitrate, iron, and silica) availability which, in turn, are caused by variability in the position of the Intertropical Convergence Zone (ITCZ) and associated changes in biogeochemical cycling and circulation in the Southern Ocean. Our multi-proxy work suggests greater scrutiny is required in the interpretation of common geochemical proxies of productivity and carbon export in the EEP.