The coupled ocean circulation‐ecosystem model MITgcm‐REcoM2 is used to simulate biogeochemical variables in a global configuration. The ecosystem model REcoM2 simulates two phytoplankton groups, diatoms and small phytoplankton, using a quota formulation with variable carbon, nitrogen, and chlorophyll contents of the cells. To improve the simulation of the phytoplankton variables, chlorophyll‐a data from the European Space Agency Ocean‐Color Climate Change Initiative (OC‐CCI) for 2008 and 2009 are assimilated with an ensemble Kalman filter. Utilizing the multivariate cross covariances estimated by the model ensemble, the assimilation constrains all model variables describing the two phytoplankton groups. Evaluating the assimilation results against the satellite data product SynSenPFT shows an improvement of total chlorophyll and more importantly of individual phytoplankton groups. The assimilation improves both phytoplankton groups in the tropical and midlatitude regions, whereas the assimilation has a mixed response in the high‐latitude regions. Diatoms are most improved in the major ocean basins, whereas small phytoplankton show small deteriorations in the Southern Ocean. The improvement of diatoms is larger when the multivariate assimilation is computed using the ensemble‐estimated cross covariances between total chlorophyll and the phytoplankton groups than when the groups are updated so that their ratio to total chlorophyll is preserved. The comparison with in situ observations shows that the correlation of the simulated chlorophyll of both phytoplankton groups with these data is increased whereas the bias and error are decreased. Overall, the multivariate assimilation of total chlorophyll modifies the two phytoplankton groups separately, even though the sum of their individual chlorophyll concentrations represents the total chlorophyll.