The state of the marine ecosystem can be estimated by a combination of numerical models and satellite observations through data assimilation (DA) methods. Satellite data representing phytoplankton chlorophyll are typically used in operational marine ecosystem prediction. These data are derived from ocean colour measured by optical satellite observations. Recently a new phytoplankton carbon product, from the ESA funded BICEP project made available from the UK CEDA Archive, has been derived through a novel processing of ocean colour. This novel carbon product captures aspects of phytoplankton biomass composition that chlorophyll alone does not represent. Here, we investigate the effects of assimilating the new carbon product on the modelling of the marine ecosystem. The investigation is carried out in a newly developed global ensemble DA system for the marine ecosystem using a coupled ocean-biogeochemistry model, NEMO-MEDUSA, and the Parallel Data Assimilation Framework. With the ensemble DA system, the evaluation can take the time-dependent uncertainty of the marine ecosystem and the reliability of the ensemble into account. We demonstrate that, compared with assimilating only the chlorophyll product, which may degrade the seasonality of phytoplankton carbon, assimilating the new carbon product can provide different patterns of adjustment and seasonal anomalies in phytoplankton concentrations, surface pCO2, and oxygen. Our findings reveal that simultaneously assimilating both phytoplankton chlorophyll and carbon products in a complex marine ecosystem yields more balanced estimates of phytoplankton biomass than assimilating a single phytoplankton product.