Security of energy supply, promotion of the bio-economy, nutrient recycling, and innovation are prioritized policy areas in the EU Strategy for the Baltic Sea Region (EUBSR). The Baltic Sea Region (BSR) has a great bioenergy potential worth exploring in this context. This paper explores the state-of-art of bioenergy systems and synergies with eco-systems services in the BSR region in the context of developing the region’s bio-economy. In this brief assessment, we consider 8 countries (i.e. Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Denmark, and Belarus) in the region. While the production and use of modern bioenergy can help reduce greenhouse gas (GHG) emissions, promote energy security, diversify energy resources, and contribute to a successful circular economy and rural development, it is important to find a balance between the exploration of resources and the management of eco-systems services. In addition, both climate change vulnerability and bioenergy production may affect the environment and the capacity of the BSR to deliver ecosystem services (ESS). We recommend integrated strategies for optimal use of bioresources in the region. Bioeconomy can be realized by innovative approaches, establishing cross-cutting institutional and policy linkages for increased prosperity and green growth in the Baltic Sea Region.