Coral reefs are one of the ecosystems most sensitive to climate change. The recent loss and degradation of coral reef ecosystems is expected to continue even if global warming is limited to 1.5°C above pre-industrial levels. There is therefore an urgent need to develop new technologies and management approaches to coral reef conservation. Emerging technologies, however, bring new challenges for decision making as they are associated with novel risks and impacts on the reef system. We argue that accounting for multiple biophysical thresholds and identifying key decisions in the planning process are crucial to avoid perverse outcomes in coral reef conservation. We identify opportunities to apply an Adaptation Pathways (AP) framework combined with a ‘values, rules and knowledge’ approach to facilitate long-term and large-scale coral reef conservation by explicitly considering uncertainty with climate change impacts in the decision-making process. The AP process can be used to reconcile the diverse values of stakeholders, scientific and cultural knowledge about the system, and the policy and regulatory context within which management must occur, in order to achieve robust long-term management.