<p>Coral reefs provide crucial ecosystem services to over 1 billion people globally and this intense pressure is causing their decline. Despite substantial investments in coral restoration and gradual advancements in coral propagation techniques, efforts focused on these ecosystem engineers are not yet fully restoring the ecological functions necessary for thriving reefs. This Perspective provides a road map for how to apply control theory to coral reef restoration, leveraging the framework’s proven effectiveness for optimizing the growth of crops and expanding it to a complex ecosystem. An in situ mesocosm called Coral Reef Arks is used as a platform to test control interventions and refine the approach. Four field experiments using Coral Reef Arks show how control interventions are used to alter ecological and environmental conditions and guide reef state factors towards desired targets. The results from these tests identify control interventions and parameter relationships that are integrated into predictive models to determine the scale at which to intervene on natural reefs. By using real-time ecological feedback, this control-based framework offers a path to identify precise, adaptable interventions that go beyond static conservation methods, providing a dynamic approach to maintain and enhance reef function in the face of ongoing environmental changes.</p>