Abstract. Recent studies indicate strengthened trade winds and intensified upwelling in the tropical Pacific since the late 1990s, suggesting implications for the biogeochemical processes. We employed a fully coupled physical-biogeochemical model to test the hypothesis that there were climate driven decadal variations in biogeochemical fields of the equatorial Pacific. We quantified changes in nitrate and iron concentrations, primary and secondary productions, and phytoplankton and zooplankton biomass between 1988–1996 and 1999–2007. Our modeling simulation showed that the intensified upwelling during 1999–2007 resulted in significant increases of nitrate and iron concentrations in the mixed layer of the central equatorial Pacific. In addition, the upwelling front moved westward, causing shifts of oligotrophic conditions to mesotrophic conditions in some parts of the western equatorial Pacific. As a result, there was an overall enhancement of biological activity in the western and central equatorial Pacific, leading to an increase in primary production and secondary production by 10–15% and 15–50%, respectively. Our study also indicated that there were changes in ecosystem states in the equatorial Pacific Ocean, suggesting alternative new states with more zooplankton biomass during 1999–2007. Additionally, our study showed significant changes in seasonal variations of biogeochemical fields. Particularly, there was a much stronger seasonality in biological production and plankton biomass near the dateline during 1999–2007 relative to 1988–1996.