Pollinators’ climate change impact assessments focus mainly on mainland regions. Thus, we are unaware how island species might fare in a rapidly changing world. This is even more pressing in the Mediterranean Basin, a global biodiversity hotspot. In Greece, a regional pollinator hotspot, climate change research is in its infancy and the insect Wallacean shortfall still remains unaddressed. In a species distribution modelling framework, we used the most comprehensive occurrence database for bees in Greece to locate the bee species richness hotspots in the Aegean, and investigated whether these might shift in the future due to climate change and assessed the Natura 2000 protected areas network effectiveness. Range contractions are anticipated for most taxa, becoming more prominent over time. Species richness hotspots are currently located in the NE Aegean and in highly disturbed sites. They will shift both altitudinally and latitudinally in the future. A small proportion of these hotspots are currently included in the Natura 2000 protected areas network and this proportion is projected to decrease in the coming decades. There is likely an extinction debt present in the Aegean bee communities that could result to pollination network collapse. There is a substantial conservation gap in Greece regarding bees and a critical re-assessment of the established Greek protected areas network is needed, focusing on areas identified as bee diversity hotspots over time.