The ocean provides us with vital climate and food services by absorbing 30% of anthropogenic carbon emissions and supplying 17% of animal proteins to the world’s population. However, we are still far from accurately estimating these services using the state-of-the-art operational models at the Copernicus Marine Environment Monitoring Service (CMEMS) Monitoring and Forecasting Centres (MFCs). The main aim of SEAMLESS is to provide CMEMS MFCs with unprecedented capabilities to deliver indicators of climate-change impacts and food security in ocean ecosystems, such as particulate carbon export and plankton phenology. The central hypothesis of SEAMLESS is that new ensemble data assimilation methods can better estimate crucial ecosystem indicators by integrating the new generation of European Copernicus satellite observations and in-situ ocean data. Specifically, our approach will link coherently biogeochemical and hydrodynamic simulations. The hypothesis is supported by our previous work, in which we improved the MFCs’ model simulations of the plankton stocks at the base of the marine food web by assimilating biogeochemical and physical data from satellites, Biogeochemical-Argo floats and gliders. SEAMLESS will develop a new assimilation prototype that will expand simulations to plankton dynamics and related biogeochemical processes, e.g., plankton phenology and carbon export. This prototype will be disseminated to CMEMS stakeholders and the wider oceanographic community. To guarantee the integration of SEAMLESS into CMEMS, we have assembled a team with outstanding expertise and track records for all the key project components, which includes CMEMS MFC core developers, and will be supported by policy, blue-growth and academic stakeholders. On project completion, six CMEMS MFCs will be able to add new and improved products on water quality, carbon cycle and trophic webs to their portfolios, ultimately allowing users to exploit more sustainably ocean ecosystem services.