This paper describes an operational protocol for integrating conservation and restoration with land-use planning in islands. Conservation challenges are intensified in insular systems due to higher ecosystem vulnerability, limited spatial options, low data availability, rapid land-use change and, globally, short-term vision planning. Our operational planning protocol integrates ecological and socio-economic factors to identify the best spatial options for conserving and restoring biodiversity, inside and outside extant reserves, while minimising future land-use conflicts. Conservation and restoration targets are formulated for species, habitats and ecological processes that support biodiversity. An optimal network of priority sites is selected to achieve those targets across the landscape. The prioritisation process integrates a Conservation Costs Index to optimise conservation and restoration investments. We discuss the outcomes of the planning protocol in terms of site prioritisation, stakeholders’ participation and general implications for spatial planning in insular systems. As with many islands, the study area of Réunion Island has experienced rapid urban and agricultural expansion, which threatens its unique biodiversity. Forty three per cent of the island is currently protected in a National Park but only half of this reserve network contributes to the achievement of targets. An additional 21% of land should be conserved mainly to ensure the persistence of ecological connections between the marine, terrestrial and freshwater realms. Finally we emphasize that our method doesn’t substitute the land-use planning debate but is aimed to better prepare the conservation sector for negotiating future land-use allocation with other socio-economic sectors in islands.