Marine protected and conserved areas (MPCAs) are promoted as an ecosystem-based adaptation (EbA) approach to increase community and ecosystem resilience to climate change. However, traditional approaches to MPCA design typically do not consider climate risk or habitat condition under a climate threat. We used the Great Sea Reef (GSR) in Fiji as a case study to develop a land-sea prioritization framework that links modeled sediment runoff from rainfall during extreme cyclone events to the probability of coral reefs being in good condition. We incorporated this information in an MPCA prioritization scenario intending to achieve 90% certainty of good-condition coral cover under cyclone risk while minimizing cost to fishers and meeting ecosystem conservation targets. We explored the trade-offs between sites selected for protection, the relative opportunity cost to fishers, and the representation of conservation feature targets between the MPCA scenario that included cyclone risk and a baseline scenario that did not. The cyclone risk scenario's best solution required larger areas of protection (5% more GSR area) than the baseline scenario and additional protection in areas with moderate to high probability of good-condition coral cover. Some areas prioritized for protection in the cyclone risk scenario had relatively high turbidity. Large sections around Vanua Levu were consistently selected for protection across both prioritization scenarios due to high concentrations of all ecosystem conservation features, particularly sea turtle feeding grounds. Overall, the cyclone risk MPCA design had a higher fisher opportunity cost but protected a larger amount of ecosystem conservation features and buffered against habitat condition uncertainty. We explored the potential outcomes of expanding on threat-avoidance and cost-effective conservation prioritization by including habitat responses to threats in the prioritization process. Our findings can inform MPCA design during EbA planning in regions at risk from climate change.