The human stomach is a bean-shaped organ that stores, mixes, and breaks down ingested food. The periodic peristaltic contractions travel along the walls driving the flow to facilitate the physical and chemical breakdown of nutrients. Experimental investigation of these processes remains challenging because in-vivo methods can only collect limited information and in-vitro approaches fail to replicate the complex physiology of the stomach. However, computational fluid dynamics (CFD) can make use of the in-vivo data and generate new insights into stomach biomechanics. In this study, we demonstrate a model of the stomach that relies on imaging data to predict the flow inside the lumen. We also incorporate the chemistry of protein hydrolysis into our model to highlight the role of the flow phenomenon in digestion. The wall motion induces jets and recirculation regions that drive the transport of the enzyme, pepsin, to expose it to unhydrolyzed protein. The species transport was diffusion dominated in the proximal region and advection dominated in the antrum of the stomach.