Climate change and biodiversity loss are global challenges that need to be addressed through a combination of measures. However, political and societal action has not yet kept pace with the urgency of these challenges. Marine carbon sequestering habitats ("Blue Carbon habitats") are globally recognized for their role in climate change mitigation and for their co-benefits and ecosystem functions, e.g., as habitat providers. In Germany, research on the Blue Carbon potential of coastal and marine ecosystems has gained momentum in recent years. However, a synergistic approach with an inclusive decision-making process is crucial to ensure political action. Current challenges are considerable knowledge gaps and the limited accessibility and transferability of existing data. Funding of research projects at different administrative levels impacts coordination, output and visibility. Here, we present a general overview of existing knowledge and identified knowledge gaps in Blue Carbon research and focus on potential Blue Carbon ecosystems (BCEs) of the German coast. Furthermore, we identify windows of opportunity and provide actionable recommendations at the science-policy-society interface by examining the current framework for Blue Carbon in Germany. Based on this, ongoing research can be further prioritized and funded in order to simultaneously strengthen the political decision-making process. The results of this study, supported by the lessons learned from a case study on the German coast, recommend a two-pronged strategy to not only avoid additional release of already stored carbon through ecosystem conservation and sustainable governance and management, but also to increase net carbon storage through (re-)establishing BCEs.