The calcareous nannofossil assemblage from ODP Site 1240 in the equatorial upwelling of the Eastern Pacific was analysed for the last 560 Ka. The chronological framework was set with a combination of isotopic stratigraphy, nannofossil biostratigraphy and one paleomagnetic event. Owing to the dominance of selected Noelaerhabdaceae taxa and Florisphaera profunda, the N index (modified from [Flores, J.A., Bárcena, M.A. y Sierro, F.J., 2000. Ocean-surface and wind dynamics in the Atlantic Ocean off northwest Africa during the last 140 000 years. Palaeogeography, Palaeoclimatology, Palaeoecology 161, 459–478]) was used to investigate the fluctuations of the nutri-thermocline in the Eastern Equatorial Pacific Ocean. This ratio measures the relative proportion of taxa that usually live in the upper photic zone in relation to those that usually thrive in the lower photic zone. Temporal changes in the relative abundances of these species over the last 560 Ka may therefore be related to variability in surface water conditions. Patterns indicated by the N index, were supported by the nannofossil accumulation rate and the total CaCO 3 coccolith content, allowing identification of four paleoceanographic intervals. Interval 1 (Marine Isotope Stage—MIS 14-8) is characterised by the highest index of paleoproductivity, maximum coccolith accumulation rates and the highest carbonate content, essentially produced by Gephyrocapsa caribbeanica. These indicators imply a strengthening of the Southern Hemisphere circulation that allowed enhanced upwelling conditions, possibly related to dominant La Niña-like conditions. Interval 2 (MIS 8-6) displays frequent fluctuations of high N index values, in agreement with the slight rise of F. profunda and the warm taxa. Both the fall in the nannofossil accumulation rate (NAR) and in the coccolith CaCO 3 content were responses to the decrease in G. caribbeanica abundance. These events are still associated with high surface productivity related to variations in intensity of the southeast Trade winds and periodically intensified upwelling, conditions related to La Niña-like events with some fluctuations. Interval 3 (MIS 5) is characterised by atypical low N values, a low NAR, and a low coccolith CaCO 3 content, suggesting that the Southern Hemisphere circulation was reduced and that the upwelling system was weakened, allowing us to infer that an El Niño-like event was the dominant condition. Finally, during Interval 4 (MIS 4-1), the system was reestablished; the N index was high again, with some inflections, and correlated with an increase in the NAR and coccolith carbonate. These indicators are related to enhance southeast trades and equatorial currents that favoured cool and nutrient-rich waters, suggesting a La Niña-like condition with some fluctuations.