Mountain communities that use local foods are more likely to be food secure over time. However, historical and contemporary policies have largely homogenized food systems by replacing diverse local foodstuffs with less diverse market-based foods. These transformations often mean that nutrition-related chronic diseases increase. We explored current and past food systems of families living in Andean landscapes in Mapuche territory, Chile. We recorded local community perceptions of food system transformations using participant observation, informal and semistructured interviews, and weekly food diary elicitation. Older participants agreed that food systems have shifted drastically since their childhoods. Food items have changed, as has the way food is procured and prepared. Perceived drivers of these changes include shifts in children's food preferences (associated with schooling and the National Food Program), the loss of cooking spaces and utensils, lack of time and temporary migration, and a decreasing production of local grains and vegetables. Food diaries (n=170 meals) collected during summer's abundance period showed that locally produced ingredients comprised 55% of families' total intake and market-based foods 45%. However, during seasonal scarcity participants reported that proportions of market-based foods increased. Rice and noodles have replaced traditional foods such as locro, soplillo, and quinwa. Participants reported an increase in diet-related chronic diseases such as type 2 diabetes, obesity, and hypertension. The Mapuche food system is facing a process of biocultural homogenization with an increase in nutrition-related chronic diseases. One major recommendation is to restructure the National School Food Program to better serve cultural particularities in Mapuche territories and to engage local experts in this rethinking. By developing new frameworks for culturally appropriate and healthy eating habits in school, children could have more access to local foods, thus strengthening traditional food systems.