Large mammals in Alaska went extinct near the end of the last ice age, but the causes remain debated. Did humans drive them extinct, or did rapid climate change disrupt their habitats? To answer this question, we studied a lake sediment core from Imuruk Lake in northwest Alaska to obtain natural “fingerprints” of past ecosystems and climate over the last 240,000 years. These fingerprints contain chemical clues of past temperature and moisture, as well as spores of dung fungus that represent the past existence of large herbivores. We document an abrupt onset of warming beginning approximately 20,000 years ago, wetter conditions, and a shift towards Pacific-derived moisture. Meanwhile, declines in grassland plants and dung fungal spores suggest that mammal populations were declining. Our findings suggest that rapid changes in temperature and moisture triggered the onset of habitat loss. This study shows how abrupt climate change can destabilize fragile Arctic ecosystems, offering lessons for understanding the risks faced by today’s Arctic wildlife in a warming world.