Global food systems are developing rapidly, and have resulted in a large burden of disease and a high proportion of environmental resource use. We combined global data sources on food supply and trade, environmental footprints, burdens of disease, and vulnerability to climate change to explore patterns from 1990 to 2017. Four distinct patterns of food supply (animal sources and sugar, vegetables and nuts, starchy roots and fruits, and seafood and oils) were matched to health and environmental risks. The animal sources and sugar pattern was found to have the greatest environmental footprint and to be associated with a greater burden of chronic disease than any other pattern, although it was also associated with lower undernutrition. This pattern is globally predominant, but has begun to decrease in higher income countries. Countries where this pattern is predominant are generally among the least susceptible to climate change, whereas more susceptible countries tend to have more sustainable patterns of food supply. More countries that are susceptible to climate change are increasingly exporting a larger proportion than before of their cereals, fruit, and vegetables globally, which will lead to increased risks in global food security. To increase resilience to future shocks, dietary change towards more sustainable patterns should accelerate in high-income countries, and the food systems of the most susceptible countries should be protected.