The spread of anatomically modern humans (AMH) into Europe occurred when shifts in the North Atlantic meridional overturning circulation triggered a series of large and abrupt climate changes during the last glacial. However, the role of climate forcing in this process has remained unclear. Here we present a last glacial record that provides insight into climate-related environmental shifts in the eastern Mediterranean region, i.e. the gateway for the colonisation of Europe by AMH. We show that the environmental impact of the Heinrich Event H5 climatic deterioration c. 48 kyr ago was as extreme as that of the glacial maximum of Marine Isotope Stage (MIS) 4 when most of Europe was deserted by Neanderthals. We argue that Heinrich H5 resulted in a similar demographic vacuum so that invasive AMH populations had the opportunity to spread into Europe and occupy large parts before the Neanderthals were able to reoccupy this territory. This spread followed the resumption of the Atlantic meridional overturning circulation at the beginning of Greenland Interstadial (GIS) 12 c. 47 kyr ago that triggered an extreme and rapid shift from desert-steppe to open woodland biomes in the gateway to Europe. We conclude that the extreme environmental impact of Heinrich H5 within a situation of competitive exclusion between two closely related hominids species shifted the balance in favour of modern humans.