A high‐resolution record of exceptionally well preserved calcareous nannofossil assemblages from Tanzania is marked by two key transitions closely related to the climatic events of the Eocene‐Oligocene transition (EOT). The first transition, at ∼34.0 Ma, precedes the first positive shift in δ18O and coincides with a distinct interval of very low nannofossil abundance and a cooling in sea surface temperatures (SST). The second, at ∼33.63 Ma, is immediately above the Eocene‐Oligocene boundary (EOB) and is associated with a significant drop in nannofossil diversity. Both transitions involve significant reductions in the abundance of holococcoliths and other oligotrophic taxa. These changes in calcareous phytoplankton assemblages indicate (1) a widespread and significant perturbation to the low‐latitude surface ocean closely tied to the EOB, (2) a potential role for reduced carbonate primary production at the onset of global cooling, and (3) a significant increase in nutrient availability in the low‐latitude surface ocean through the EOT.