Beyond the individual content in nutrients, it is now established that the matrix structure is also to consider when evaluating the nutritional properties and possible health effects of a food material. The objective of this study was to gain knowledge on the effect of the structure of dairy products on the digestion of milk proteins as inferred from a mathematical modelling of mini-pig in vivo data. Six dairy matrices of the same composition but differing by their physicochemical and structural properties were investigated. They were manufactured using technological processes commonly used in the industry (heat treatment,rennet gelation, acid gelation and mixing). The experimental results cover a 7 h postprandial period and consist in plasmatic amino acid concentrations as well as dry matter contents and chromium concentrations (a marker of the liquid phase of the meal) of samples collected at the stomach exit. The model developed not only accounts for the main digestive events but also for phenomena that can occur within the stomach (milk clotting and aggregate syneresis). It provides a good fitting of all the experimental data and allows estimating parameter values that can be explained by considering the properties of the matrices investigated. The model has also been used to estimate quantities that cannot be observed experimentally (stomach volumes, endogenous secretions, gastric emptying half-time...) in order to recover a better picture of all the results and validate the model predictions against literature. It even appears that our simulations of gastric emptying and aminoacidemia superimpose very well with previously published data obtained using similar matrices and the same mini-pig species. This study shows that the great differences in the kinetics of amino acid absorption that were observed experimentally can be fully understood by considering the behaviour of the dairy matrices within the stomach. It therefore offers interesting perspectives for the integration of food structure parameters, and more particularly for dairy products, in the comprehensive view of the nutritional quality of food products.