Aquatic food systems play a critical role in supporting food security globally, with many people depending on these systems for nutrition and livelihood development through job opportunities in different value chains in the fisheries sector. The potential of these systems has been derailed by several challenges, including climate change, human factors like overexploitation of resources, and unavailability and access to the aquatic foods, in addition to limited markets. Food security can only be achieved if we have a safe, steady, and healthy supply of food that meets the consumer. Through workshop discussions that brought together diverse stakeholders and employed different methodologies, this paper seeks to understand and bring to light these challenges and how best to mitigate the shortcomings that lead to the under-recognition as well as underperforming of aquatic food systems compared to other food systems despite their nutritional significance. The communique on the “Sustainable Agri-Food Systems Intelligence – Science-Policy Interface” (SASi-SPi) was organized in partnership with various research/ academia, stakeholders in the blue economy sector, and hosted by the Kenya Marine and Fisheries Research Institute (KMFRI). After a strong two-day session involving the pitching of ideas from different individuals, consensus was reached on the resolutions that will drive the agenda of the aquatic food systems forward. The session was unique since it was community-centered, with the policy influencers giving more airtime to the small-scale fishers to articulate the challenges they termed perennial in the industry and voting to bring equity into play. The strategic recommendations included making finances that are sustainable available, enhancing the capacity of non-fishing communities to consume aquatic value-added products by taking advantage of sensitization and campaigns, leveraging technology to develop the sector, and gender inclusion, allowing women to have seats on the decision-making table. Through the integration of equitable access, nutrition value, and sustainable resource usage in aquatic food systems, we can provide transformative action aimed at sustainably using our aquatic systems.