The stomach and intestines play an important role in homogenizing the contents of the tract, mixing food with enzymes. The study of digestion processes in a fed state remains difficult by experimental methods. Using computational fluid dynamics models it is possible to obtain flow characteristics at any point in the computational domain. At the previous stages of research, we developed a model to describe the flow of a multiphase multicomponent mixture in the antroduodenum, taking into account the processes of mass transfer between phases, biochemical reactions, mass sources and effluents. In this article, we propose an improvement of the model for describing the multiphase flow in the whole stomach and duodenum, taking into account the gas phase. The mathematical formulation of the problem includes the balance equations of mass and momentum for a multiphase medium with mass sources. Boundary conditions take into account the peristalsis of the tract. In numerical experiments we studied the influence of the density of food particles on the distribution of volume fractions of phases, mass fractions of food components and enzymes, pH level in the digestive tract. In the future, it is necessary to continue working with the rheological properties of the flow.