Wallis, Alofi, and Futuna are three small islands in the central Pacific Ocean, characterized by different reef geomorphologies. Following a request from the local Environment Service, we developed an indicative conservation plan for each island with two objectives: (1) representing 20% of the extent of each coral reef habitat within no-take areas while (2) keeping all subsistence fishing grounds open for extraction. The first objective was more ambitious than the current Convention on Biological Diversity (Aichi) targets. We found that both objectives could not be achieved simultaneously and that large compromises are needed. Due to the small size of these islands, and the dependence of local communities on coral reef resources, the fishery objective significantly limited the extent of most habitats available for conservation. The problem is exacerbated if the conservation plan uses larger conservation units and more complex habitat typologies. Our results indicate that international conservation guidelines should be carefully adapted to small Pacific islands and that incentives to make feasible the necessary reductions in available fishing grounds will probably be needed.