Two model simulations were performed to address the influence of the Indonesian throughflow (ITF) on the biogeochemical state of the equatorial Pacific. A simulation where the ITF is open is compared with an experiment where it is closed, and it is first shown that the impacts on the physical circulation are consistent with what has been found in previous modelling studies. In terms of biochemistry, closing the ITF results in increased iron concentration at the origin of the Equatorial Undercurrent (EUC). But the 11Sv of water otherwise transferred to the Indian Ocean remain in the equatorial Pacific, which result in a 30 m deepening of the thermocline/ferricline in the eastern Pacific. This deepening decreases the iron concentration of the equatorial wind driven upwelled water and cancels the iron increase advected by the EUC. The iron decrease of the equatorial upwelled water leads to decrease primary production by 15% along the equator.