Coral reefs are highly vulnerable habitats, threatened by climate change and local anthropogenic impacts. Management is imperative, and spatial prioritisation apportions the area of interest to inform investments of scarce conservation resources. Spatially delineated planning units used to make management decisions are typically large enough to contain significant natural variabilities, but the ecological significance of such variance is seldom considered in planning decisions. On coral reefs, the patchiness of habitat quality within planning units matters both ecologically and functionally. Here, we show that considering within-planning unit variance in spatial prioritisation influences the location and design of reserve networks. Studying Timor-Leste, we statistically model the average and variance in coral cover. We compare conservation priority areas for scenarios informed by coral cover and variance to a baseline scenario with the spatial prioritisation software Marxan. To further explain these differences, and to show the value of including coral variance as a metric in spatial prioritisation, we created a reserve quality score. We show that the similarity between reserve networks was only 57% for protection, and 44% for restoration objectives. For both objectives, the inclusion of cover variance improves the conservation benefit of management. This project has shown a novel way to target areas for restoration. These results demonstrate that not only is mean coral cover (and, by extension, reef condition) a key criterion in selecting marine conservation actions, but its variance must be considered in spatial conservation prioritisation to improve both the efficiency and benefit of management actions within marine reserve networks.