After recognizing the importance of marine and coastal resources and the use of marine space for economic growth, the European Union (EU) created and implemented a long-term Blue Economy (BE) strategy that supports the development of traditional and emerging marine and maritime sectors, aiming at the enhancement of Blue Growth (BG). However, despite the existence of a robust policy framework that supports the expansion of BE sectors at both an EU Sea Basin and state level, scholars have been sceptical as to whether the pursuit of BG adequately addresses the challenges that usually come with economic development, including those of climate change and marine biodiversity loss. Various frameworks for integrating sectoral goals with each other and with environmental goals that could facilitate the transition towards Sustainable Blue Growth (SBG) already exist and have been suggested and promoted by the European Commission, such as Ecosystem-Based Management (EBM) and Marine Spatial Planning (MSP). They require the consideration of marine ecosystems and biodiversity and their protection as one of the BE sectors to be integrated via planning and management, which in turn requires the estimation of the value of ecosystem services and the spatial implications thereof. Nonetheless, there is little evidence or real-world examples on whether and how ecosystems, and within them coastal and marine biodiversity, are actually integrated (i.e., mainstreamed) when developing sectoral policies and planning and implementing economic activities at sea at various scales, i.e., local, national, and regional, and what the necessary steps and actions are that would facilitate such mainstreaming. By seeking evidence in EU and Atlantic Arc (AA) member states’ sectoral policies on marine tourism, ports and shipping, marine renewable energy, and fisheries and aquaculture (as promoted by the Atlantic Maritime Strategy and its corresponding action plans) and in the outcomes of the Interreg Atlantic Funded Research Project MOSES (aiming at valuating a Sustainable Blue Economy at the national and regional scale of the EU AA), the present article focused on understanding if and how marine biodiversity is taken into consideration by EU and AA BE and/or BG policies, strategies, and sectoral developments. Τhe selected sectoral policies demonstrate a good uptake of marine-ecosystem- and biodiversity-related challenges; however, at both the EU and the AA member-state level, it is unclear whether and how marine ecosystems and biodiversity are addressed as a separate BE sector. As such, we argue why and how Marine Biodiversity Mainstreaming (MBM) could address this gap, and hence it could contribute to planning, implementing, and managing maritime economic activities towards SBG at the Sea Basin level. This is demonstrated by illustrating the central role of MBM in enabling (and being further enabled by) the above integrative frameworks (i.e., MSP and EBM) and by presenting the key elements and actions required for such facilitation.