Coral atoll islands, common in tropical and subtropical oceans, consist of low-lying accumulations of carbonate sediment produced by fringing coral reef systems and are of great socio-economic and ecological importance. Previous studies have predicted that many coral atoll islands will become uninhabitable before the end of this century due to sea level rise exacerbating wave-driven flooding. However, the assumption that such islands are morphologically static, and will therefore ‘drown’ as sea levels rise, has been challenged by observations and modelling that show the potential for overwashing and sediment deposition to maintain island freeboard. However, for sustainable habitation, reliable predictions of island adjustment, flooding frequency and the influence of adaptation measures are required. Here, we illustrate the effect of various adaptation measures on the morphological response of an atoll island to future sea level rise using process-based model simulations. We found that the assumption of a static island morphology leads to a significant increase in the predicted frequency of future island flooding compared to morphodynamically active islands, and demonstrate that natural morphological adjustment is a viable mechanism to increase island freeboard. Reef adaptation measures were shown to modify the inshore wave energy, influencing the equilibrium island crest height and therefore the long-term morphological response of the island, while beach restoration mainly delays the island’s response. If embraced and implemented by local communities, allowing for natural island dynamics and implementing well-designed adaptation measures could potentially extend the habitability of atoll islands well beyond current projections.