Most studies on the impact of climate change on foods focus on the consequences to security and safety. In the present study we provide scientific evidence on an overlooked aspect of climate change related to the microbiological stability of foods. Most microbiologically stable processed foods are contaminated with spores of thermophilic spoilage bacteria which are highly heat-resistant and can survive thermal processing. Current temperatures during distribution and storage in temperate climates do not allow growth of thermophilic bacteria to levels that can cause spoilage, ensuring their microbiological stability. Our findings suggest that the latter limiting condition can be eliminated by global warming. By assessing different global warming scenarios for 38 European cities in a case study with canned milk, we show that failing to achieve the 2 °C target for climate change can lead to a very high risk of spoilage and cause a collapse of the shelf-stable food chain.