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 from optical satellite observations. Recently a novel phytoplankton carbon product, from the ESA funded BICEP project available from the UK CEDA Archive, has been derived through an alternate processing of ocean colour. With the novel carbon product, the phytoplankton biomass is represented more directly than relying on the chlorophyll. 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 solely assimilating chlorophyll product, with the new carbon product the DA can provide different patterns of adjustments in the phytoplankton concentration and seasonal anomalies. Our findings reveal that simultaneously assimilating both phytoplankton chlorophyll and carbon products in a complex marine ecosystem yields more accurate and balanced estimates of phytoplankton biomass than assimilating a single phytoplankton product.