Diatoms play an essential role in marine biogeochemical cycles by their large contribution to primary production and particle export. Under nutrient limitation, diatom biomass often exhibits large deviations from the Redfield ratio. Here a biogeochemical ocean general circulation model is applied to investigate the influence of variations in diatom stoichiometry. The ecosystem model allows for variable Chl:C:N:Si stoichiometry in phytoplankton biomass regulated by light and availability of macronutrients (nitrate, silicic acid) and iron. Two size classes of phytoplankton are considered with the larger representing diatoms. After 5 years of simulation, the surface distributions of both phytoplankton groups are in a reasonable cyclostationary state. Compared to the ‘steady’ state, a sensitivity simulation with fixed diatom stoichiometry for Si:N of 1.2:1 showed a slight shift from small phytoplankton to diatoms leading to a shift in primary production between two groups. Total primary and export production were conservative, indicating a tendency for compensation. In the Southern Ocean, less opal production and decreased particle export ratio of Si:N resulted in raising silicic acid to the south of Subantarctic Front elucidating the importance of decoupling of different elemental cycles.