Mangroves are an important ecosystem that provides valuable social, economic, and environmental services. Indonesia has placed mangroves on its national priority agenda in an important effort to sustainably manage this ecosystem and achieve national climate commitments. However, mangrove management is faced with complex challenges encompassing social, ecological, and economic issues. In order to achieve the government’s commitments and targets regarding mangrove restoration and conservation, an in-depth study on and critical review of mangrove management in Indonesia was conducted herein. This work aimed to provide a comprehensive analysis of the challenges and strategic recommendations for sustainable mangrove management in Indonesia. SWOT analysis was carried out to understand the strengths, weaknesses, opportunities, and threats related to mangrove management in Indonesia. To address these gaps, we reviewed the existing policies, current rehabilitation practices, environmental challenges, and research and technology implementations in the field. We found that strategies on mangrove ecosystem protection, such as improving the function and value of mangrove forests, integrating mangrove ecosystem management, strengthening political commitments and law enforcement, involving all stakeholders (especially coastal communities), and advancing research and innovations, are crucial for sustainable mangrove management and to support the national blue carbon agenda.