Coastal climate change impacts challenge policy and decision makers to adopt more effective adaptation measures. The ecosystem-based management approach can shift adaptation towards a more holistic, integrated and sustainable path. However, as countries work on strategies to adapt to climate change, the questions of if and how such agendas consider and operationalise ecosystem-based management remains. As one of the world’s largest coastal countries, Brazil can have a prominent role in advancing the implementation of ecosystem-based management to coastal zones. By analysing two national Brazilian climate change adaptation institutions, this article evaluates and discusses the country’s advances in promoting climate change adaptations based on ecosystem-based management principles. Our findings show that, although Brazil has incorporated many ecosystem-based management principles to climate change adaptation at the national level, greater attention should be given to operationalizing principles related to acknowledging uncertainties, sustainability, democracy and knowledge production and application. The challenges to implement these principles mirror historical challenges of Brazilian coastal management policies, such as balancing development and conservation, promoting social participation and implementing effective social-ecological assessments and monitoring programs. Policy makers, scientists and communities should be aware of the need to strengthen ecosystem-based management principles in the current adaptation agenda in order to enhance its capacity to foster adaptation and just coastal sustainability.