The blue bioeconomy offers promising pathways for sustainable marine resource management, yet its development faces significant governance challenges. This study examines how governance structures can enable or hinder innovation in emerging blue bioeconomy systems, focusing on the valorisation of fishery side-streams and microalgae development. Using a novel Governance of Innovation Systems (GOIS) framework adapted from Technological Innovation Systems theory, we analyse governance structures across four European regions: Sicily (Italy), Saaremaa (Estonia), Greenland and West Jutland (Denmark). Through desk research and 18 stakeholder interviews, we identify key barriers and enablers within six governance functions: knowledge development, direction of search, legitimacy creation, resource mobilisation, market formation and entrepreneurial experimentation. Our findings reveal that while market formation shows promise across regions, significant challenges persist in legitimacy creation and knowledge development. Regulatory complexity and fragmented responsibilities emerge as primary barriers to innovation, particularly affecting small and medium-sized enterprises. Resource constraints manifest differently across regions, from infrastructure limitations in Sicily to workforce shortages in Denmark and Estonia. Based on these insights, we propose three key policy interventions: regulatory process simplification through sandboxes and administrative one-stop shops, innovative financing mechanisms including blue bonds and accelerator programs, and enhanced collaborative frameworks through regional networks and public-private partnerships. This study contributes to innovation systems theory and practice by demonstrating how systematic analysis of governance functions can inform targeted interventions to support sustainable blue bioeconomy development.