Identification of important habitats of charismatic marine megafauna is essential to enhance our conservation capacity. Still, for species such as sea turtles that have a long-life span, a complex life history and a highly migratory nature, spatially delineating important marine areas is not a simple task. Even in the case that such areas are identified, our ability to draw effective measures and propose conservation prioritization schemes faces additional challenges, due to the dynamic climate-driven redistribution of habitats. Here, we compile a database on foraging locations of loggerhead sea turtles across the Mediterranean Sea and use climatic niche models to predict the distribution of foraging grounds for juvenile and adult life stages. We explore potential shifts due to future changes in ocean temperature and identify sites, considered as important for both life stages, that will persist under climate change. We found extensive areas which could host foraging sites for juvenile loggerheads, distributed at the central and western Mediterranean, while adults’ foraging grounds had a more sparse and patchy distribution, mostly at the central and eastern part of the basin. Under future changes, expansions prevail over contractions, but projected redistribution of foraging space for both life stages will probably lead to remarkable losses of climatic suitability at certain sites. The coverage of important areas, hosted primarily at the neritic zone, will be extended in the future. Our analyses add a missing dimension to conservation efforts, related to the basin-wide distribution of important areas, offering novel insights towards incorporating climate change into conservation planning.