We investigated middle Miocene–Pleistocene deep-sea benthic foraminifera from IODP Hole U1338B in the eastern equatorial Pacific (EEP). Starting at ~12 Ma, periodic constriction and closure of the Central American Seaway and resulting productivity fluctuations led to distinct changes in benthic foraminiferal composition at 9.5, 5.6–5, 4.5, and 2.1 Ma in the EEP. A temporal increase in high-productivity taxa, known as the late Miocene–early Pliocene “biogenic bloom,” produced a high organic flux to the seafloor from 6.4–5.4 Myr. Our results suggest that, while overall productivity increased at that time, seasonal inputs of phytodetritus did not until after 4.5 Ma, when upwelling, recognized by an abrupt rise in Epistominella exigua, increased during another constriction of the Central American Seaway, marking the beginning of modern oceanographic conditions in the EEP. Although foraminiferal diversity increased during the late Miocene–early Pliocene biogenic bloom, it was not enhanced by the high phytodetrital input from 4.5–3 Myr.