Crown-of-thorns starfish (CoTS) are major coral predators on the Great Barrier Reef and are managed through manual control (culling). Knowledge gaps encompass manual control efficacy, interactions with perturbations, and how to best deploy efforts to improve coral trajectories given local conditions. Through Models-of-Intermediate-Complexity-for-Ecosystem-assessment (MICE), we examined manual control efficacy under bleaching, cyclone, and CoTS outbreak conditions. We found control could improve coral cover up to 14% and shorten outbreak duration 2-4 years. Culling CoTS to very low levels had poorer outcomes across all sites due to resource constraints and diminishing returns. Simulations showed culling was most effective where corals were less susceptible to thermal stress, experienced lower accumulated thermal stress, and under reduced CoTS recruitment. These varied among and within reefs, hence heterogenous locally tailored management works best. Our recent MICE application informs coral-CoTS based control targets and where these could benefit from additional supporting information. Ongoing work is exploring the potential role of CoTS behaviour in manual control and for linking with other intervention strategies (e.g. predator control). Our work underscores the importance of managing pest species interactions with ecological assets rather than purely focusing on the pest species.