Based on insights from an ongoing research project on food sustainability, we argue that discussing sustainable diets in isolation from food systems poses risks. Among these risks are making healthy diets exclusive, or ignoring externalities like biodiversity loss, land concentration, and encroachment on commons. Case studies from Bolivia and Kenya show how marked shifts from traditional to more uniform diets rich in sugar, salt, and fatty acids come with a radical transformation of food systems. Systems formerly based on local knowledge, local inputs, and local labor relations become dependent on external inputs, heavy mechanization, and productive specialization. Making diets more sustainable requires policies that protect existing and strengthen new forms of family and community farming. We discuss critical links between sustainable diets and sustainable food systems with reference to five principles of food sustainability: food security, the right to food, reduction of poverty and inequality, environmental performance, and resilience. Our analysis provides a basis for more comprehensive research and policies that minimize trade-offs and maximize synergies between sustainable diets and food systems.