Climate change is a major threat to global biodiversity, although projected changes show remarkable geographical and temporal variability. Understanding this variability allows for the identification of regions where the present-day conservation objectives may be at risk or where opportunities for biodiversity conservation emerge. We use a multi-model ensemble of regional climate models to identify areas with significantly high and low climate stability persistent throughout the 21st century in Europe. We then confront our predictions with the land coverage of three prominent biodiversity conservation initiatives at two scales. The continental-scale assessment shows that the most instable future climate in Europe is likely to occur at low and high latitudes, with the Iberian Peninsula and the Boreal zones identified as prominent areas of climatic instability. A follow-up regional scale investigation shows that robust climatic refugia exist even within the highly exposed southern and northern macro-regions. About 23–31 % of assessed biodiversity conservation sites in Europe coincide with these identified climatic refugia, we contend that these sites should be prioritised in the formulation of future conservation priorities as the stability of future climate is one of key factors determining their conservation prospects. Although such focus on climate refugia cannot halt the ongoing biodiversity loss, along with measures such as the resilience-based stewardship, it may improve the effectiveness of biodiversity conservation under climate change.