Since 1990 the Yanaconas indigenous, located in six departments of Colombia, passed through drastic changes in the food systems. This study analyze the changes of these systems from 1980, decisive factors of these changes and the consequences in the population health. The case study was executed in the Guachicono Indigenous Reservation, which form the Yanacona Community with other 30 communities. The participant observation, the interviews, mind maps, focal groups and the time line were the techniques used in the field work. They were three systems which existed between 1980 and 2015. The self-consumption feeding was the system between 1980 and 1990. The features were the local production, the existence of social practices for the food interchange without any money, consuming four meals per day. The bonanza poppy was the system between 1990 and 2000; characterized by food production almost null, the increasing in the food trade from external sources, consuming five meals per day. Back to the origins was the food system which is being created since 2000; it's in the middle of a set of changes which looks for a rescue of the culture values and the food autonomy of the Reservation.The main decisive factors of these changes were the armed conflict and the poppy cultivation, aerial spraying with glyphosate, Government National policies and the internal political and administrative organization. We can mention some consequences on the population health thanks to the changes in the food system: the increasing of the high risk pregnancies, low birth weight, malnutrition in children, overweight and hypertension in adults. Stomach diseases and cancer cases are recorded from 2000; the State actions to eliminate illicit crops did not consider the social and environmental implications. The qualitative analysis indicates there is food insecure mainly determined by the quality of the food consumed. However, there is an internal organizational political process in the Yanacona Community that includes the rescue of the traditional diet, which leads to the conclusion that Yanaconas travel the road in search of food autonomy.