We will map the optimal locations for Marine Protected Areas (MPA) in European seas using measures covering the range of biodiversity from species to ecosystems, including habitats. The contribution of these measures to carbon storage will be quantified and mapped. The top 10% and 30% of the area that includes most species, habitats, and ecosystems, and maximises blue carbon benefits, will be prioritised as an MPA network. The geographic scope is the Atlantic Exclusive Economic Zones of the EU and its neighbours, and all of the Mediterranean, Baltic and Black Seas. Feedback from Marine Spatial Planning (MSP) stakeholders in the regional seas on the proposed MPA network and methodology will be reported. A first data-driven classification of ecosystems in European seas will use environmental data from Copernicus and EMODnet. Environmental niche models will map thousands of species and biogenic (fauna and flora structured) habitat ranges and add to existing seabed habitat maps in EMODnet. Analyses of spatial relationships between biodiversity measures and evidence of carbon storage will support the prioritisation analyses. Parallel modelling of current connectivity and the velocity of climate change will map connectivity within the proposed MPA network and how it will accommodate species distribution shifts due to anthropogenic climate change. All data and maps will be freely available through EMODnet, the Ocean Biodiversity Information System, EC Knowledge Centre for Biodiversity, and the project’s online atlas. The atlas will provide transparency, traceability and enable reproducibility of the results. Its synthesis will show stakeholders (MSP, NGO, students, researchers) why areas have been prioritised. The use of decision support software will enable alternative network designs based on stakeholder preferences and could thus support wider MSP beyond the subject and study area.