Unravelling the fate of food in the gastrointestinal tract is essential to better understand the health effects of food and fight against diet-related pathologies such as cardiovascular diseases and type-2 diabetes, and enable the design of food of high nutritional and sensory qualities to provide humans with a healthy diet. Research to date has mostly considered foods according to their composition. However, the role of the food matrix, Le. the microstructure-level organization of nutrients and their interactions, in the digestive process was recently demonstrated. This paper summarizes the work done by different groups at the INRA to understand and model food digestion. Integration of the knowledge acquired will serve the development of a reverse engineering approach to design new foods purpose-adapted to meeting the nutritional needs of specific populations like infants or the elderly.