The Eocene‐Oligocene transition (EOT; ∼34 Ma) was one of the most prominent global cooling events of the Cenozoic, coincident with the emergence of continental‐scale ice‐sheets on Antarctica. Calcareous nannoplankton experienced significant assemblage turnover at a time of long‐term surface ocean cooling and trophic conditions, suggesting cause‐effect relationships between Antarctic glaciation, broader climate changes, and the response of phytoplankton communities. To better evaluate the timing and nature of these relationships, we generated calcareous nannofossil and geochemical data sets (δ18O, δ13C and %CaCO3) over a ∼5 Myr stratigraphic interval recovered across the EOT from IODP Site U1509 in the Tasman Sea, South Pacific Ocean. Based on trends observed in the calcareous nannofossil assemblages, there was an overall decline of warm‐oligotrophic communities, with a shift toward taxa better adapted to cooler more eutrophic conditions. Assemblage changes indicate four distinct phases caused by temperature decrease and variations in paleocurrents: late Eocene warm‐oligotrophic phase, precursor diversity‐decrease phase, early Oligocene cold‐eutrophic phase, and a steady‐state cosmopolitan phase. The most prominent shift in the assemblages occurred during the ∼550 kyr‐long precursor diversity‐decrease phase, which has relatively high bulk δ18O and %CaCO3 values, and predates the phase of maximum glacial expansion (Earliest Oligocene Glacial Maximum–EOGM).