The Alboran Sea, located at the western Mediterranean Sea, hosts a diverse and ecologically important cetacean community, including endangered species. However, current marine protected areas (MPAs) in the region are limited in scope, and existing conservation strategies are insufficient to address the wide-ranging ecological needs of cetaceans. This study aims to synthesise existing national and international conservation initiatives in the Alboran Sea, develop a prioritization framework and propose a global protection framework for the basin. Our main results highlight that the Alboran Sea presents diverse protection figures including multiple sites of community importance (SCI) for the conservation of cetaceans, as well as it has been designated a cetacean critical habitat, and three different important marine mammal areas (IMMAs) have been identified. In addition, by using species distribution models and a prioritization approach, we identified key areas requiring enhanced protection for multiple cetacean species. The prioritization analysis considered various conservation scenarios, including minimising area costs and accounting for human threats such as fishing and pollution. Three critical areas emerged from our analysis, bridging existing SCIs. So, in this context, we propose the establishment of new protected areas in the northern site of the basin and advocate for a large-scale marine sanctuary—the Mediterranean Gate Sanctuary—due to the overlap of several national and international proposals for protection. A threat-based, species- and space-oriented conservation approach is recommended to effectively safeguard the region's biodiversity. By fostering stakeholder engagement and transnational collaboration, this sanctuary could address the ecological challenges cetaceans face and ensure sustainable marine management in the Alboran Sea.