Temperate reefs from around the world are becoming tropicalised, as warm-water species shift their distribution towards the poles in response to warming. This is already causing profound shifts in dominant foundation species and associated ecological communities as canopy seaweeds such as kelp are replaced by tropical species. Here, we argue that the cascading consequences of tropicalisation for the ecosystem properties and functions of warming temperate reefs depend largely on the taxa that end up dominating the seafloor. We put forward three potential tropicalisation trajectories, that differ in whether seaweeds, turf or corals become dominant. We highlight potential gains to certain ecosystem functions for some tropicalisation endpoints. For example, local benthic fish productivity may increase in some tropicalised reefs as a higher proportion of primary production is directly consumed, but this will be at the expense of other functions such as carbon export. We argue that understanding these changes in flows of energy and materials is essential to formulate new conservation strategies and management approaches that minimise risks as well as capture potential opportunities. Regardless of which trajectory is followed, tropicalised systems represent largely novel ecosystem configurations. This poses major challenges to traditional conservation and environmental management approaches, which typically focus on maintaining or returning species to particular locations. We outline management practices that may either mitigate predicted structural and functional changes or make the most of potential new opportunities in tropicalised reefs. These include marine protected areas to increase resilience and connectivity, the development of new fisheries that target range-expanding invaders, and assisted evolution and migration strategies to facilitate the dominance of large habitat formers like corals or seaweeds. We highlight important ecological and ethical challenges associated with developing novel approaches to manage tropicalised reefs, which may need to become increasingly interventionist. As technological innovations continue to emerge, having clear goals and considering the ethics surrounding interventions among the broader community are essential steps to successfully develop novel management approaches. A plain language summary is available for this article.