We aimed to assess the social-ecological roles of marine alien species in the eastern Mediterranean Sea – a global hotspot of bioinvasions and local extinctions – and their potential contribution to reaching Targets 1, 3, 10, and 11 of the Kunming-Montreal Global Biodiversity Framework (GBF). We employed a comprehensive methodology, incorporating a literature review, fish surveys, and a consumer behavior questionnaire. Furthermore, we applied spatial conservation prioritization to identify reef fish conservation areas, both with and without considering marine alien species. Our findings reveal the dual role of alien species, with both adverse and beneficial effects on biodiversity, ecosystem functions, and services. Based on our analyses, we advocate for a paradigm shift in conservation, moving beyond the traditional focus solely on native biodiversity to include alien species as contributors to ecosystem functionality and services, especially in regions where native biodiversity is rapidly declining due to ocean warming. Our results highlight the importance of integrating alien species considerations into conservation planning to achieve GBF targets 1 and 3, emphasizing their potential to maintain and enhance ecosystem services, such as food provision through fisheries (GBF Targets 10 and 11), amidst rapid climate change. We present a framework for incorporating both the positive and negative aspects of alien species into Systematic Conservation Planning to guide conservation investments efficiently. By adopting a pragmatic, holistic approach to conservation and recognizing the diverse impacts of alien species, decision-makers could more effectively achieve GBF Targets 1, 3, 10, and 11 in the eastern Mediterranean.