The oldest known hominin remains in Europe [~1.5 to ~1.1 million years ago (Ma)] have been recovered from Iberia, where paleoenvironmental reconstructions have indicated warm and wet interglacials and mild glacials, supporting the view that once established, hominin populations persisted continuously. We report analyses of marine and terrestrial proxies from a deep-sea core on the Portugese margin that show the presence of pronounced millennial-scale climate variability during a glacial period ~1.154 to ~1.123 Ma, culminating in a terminal stadial cooling comparable to the most extreme events of the last 400,000 years. Climate envelope-model simulations reveal a drastic decrease in early hominin habitat suitability around the Mediterranean during the terminal stadial. We suggest that these extreme conditions led to the depopulation of Europe, perhaps lasting for several successive glacial-interglacial cycles.