The Mediterranean Basin is a critical biodiversity hotspot hosting numerous bird species that are likely to be sensitive to climatic changes. This study integrates ecological niche modeling and Bayesian skyline plot analyses to assess the historical, current, and future geographic distributions, and population dynamics of 45 endemic bird species in the region. Using occurrence data from the Global Biodiversity Information Facility and climate scenarios ranging from the Last Interglacial, Last Glacial Maximum, mid-Holocene, and present to projections for 2050 and 2070 under representative concentration pathways (RCPs) 2.6, 4.5, and 8.5, we modeled species geographic distributions to characterize shifts in climatic suitability. Our results reveal significant distributional changes corresponding to past climatic fluctuations, with contractions during the Last Interglacial and Last Glacial Maximum into refugial areas, and expansions during the mid-Holocene. Current species richness maps align closely with known biodiversity hotspots in the Mediterranean. Future projections indicate a northward shift in species’ distributions, with potential losses in habitat suitability in central Iberia under higher emissions scenarios. BSP analyses demonstrate increases in effective population sizes following the Last Glacial Maximum. These findings highlight the complex interplay between climate change and avian population dynamics, emphasizing the necessity of incorporating climatic factors into conservation strategies to preserve the rich avian diversity of the Mediterranean Basin.