This study deals with the future of the traditional agroforestry systems (TAFSs) in the northern Mediterranean Basin. Important productive systems, such as ancient non-irrigated olive groves and extensive silvopastoral systems, from subalpine grasslands to coastal landscapes, are being irreversibly degraded, threatening the bio-cultural heritage of the Mediterranean region, an area recognized as a global biodiversity hotspot. In the midst of the global biodiversity and climate crisis, immediate actions are proposed for the protection and conservation management of TAFSs, within a new EU policy framework. Having the TAFSs of Greece in the spotlight of this analysis, a four-step approach was used in order to review the value of agroforestry in terms of (a) biodiversity (birds, mammals, invertebrates and soil biota), (b) agroforestry landscapes, such as traditional olive groves on terraces and valonia silvopastoral systems, (c) ecosystem services, especially concerning cultural values, and (d) the modern threats to traditional agroforestry. Through this research, problems are highlighted and European policy priorities are defined. Our conclusion is that there is an immediate need to revise the European Union rural, forestry, and environmental policies in the Mediterranean region, following the provisions of the new EU Nature Restoration Law, in order to revive agroforestry landscapes and make them productive and sustainable again for the benefit of rural economies, local communities, and biodiversity, especially in marginal Mediterranean mountainous and island areas, where depopulation and susceptibility to wildfires are major threats.