The management of mangroves, seagrasses and salt marshes, collectively known as “blue carbon ecosystems” (BCEs) is significant because of global contribution to climate change mitigation while delivering co-benefits (e.g., food source, coastal protection) at the local level. However, despite their diverse ecosystem services, BCEs are continuously subjected to anthropogenic (e.g., land-use conversion) and natural (e.g., typhoons) threats which in turn result in the reduction or loss of their important services. In the context of climate change, there degradation could result to the increase of carbon dioxide in the atmosphere. Thus, the blue carbon concept has now reached international prominence and gained attraction from diverse groups of individuals including the scientific community, non-government organizations, intergovernmental bodies, and policymakers to conserve and protect, and to provide science-based recommendations for policy and management strategies of BCEs. Through the Asia-Pacific Network for Global Change Research (APN) funding, which supports global change research on climate mitigation, this project contributed to BCEs management from local perspectives of social and policy sciences which are largely overlooked, yet, integral parts of sustainability. Through a collaborative approach from scientists and national-to-local governmental bodies, with aspirations from Sustainable Development Goals (SDGs) and APN goals, a series of capacity development workshops was conducted in the Philippines and Indonesia. Results of the workshops highlighted that there are multiple factors to be identified and understood in enhancing stakeholders’ capacity. These included their perceptions, personal views or experiences, and external influencers (e.g., social media, non-government organizations). Availability and accessibility of capacity development tools was documented to be critical for local stakeholders to be more independent from external organizations. These workshops highlighted that by involving local stakeholders in climate change discussion, they are more likely to participate in various BCE management activities. Moreover, including them in scientific investigations empowers them, and making the research results more beneficial to community. Their participation to data generation can inform them on the importance of science-based activities and user-friendly decision-support guidelines.