Biogeochemical processes play an important role in ocean environments and can affect the entire Earth’s climate system. Using an ocean-biogeochemistry model (NEMO-TOPAZ), we investigated the effects of changes in albedo and wind stress caused by phytoplankton in the equatorial Pacific. The simulated ocean temperature showed a slight decrease when the solar reflectance of the regions where phytoplankton were present increased. Phytoplankton also decreased the El Niño-Southern Oscillation (ENSO) amplitude by decreasing the influence of trade winds due to their biological enhancement of upper-ocean turbulent viscosity. Consequently, the cold sea surface temperature bias in the equatorial Pacific and overestimation of the ENSO amplitude were slightly reduced in our model simulations. Further sensitivity tests suggested the necessity of improving the phytoplankton-related equation and optimal coefficients. Our results highlight the effects of altered albedo and wind stress due to phytoplankton on the climate system.