Protein Digestion Yah! You are right that stomach is responsible for digestion of protein which does not begin until in the stomach, we will begin there. In the mouth, vigorous chewing of high-fiber foods slows eating and stimulates the flow of saliva. The salivary enzyme amylase starts to work on carbohydrates hydrolyzing starch to shorter polysaccharides and to maltose. Because we are addressing the digestion of protein which does not begin until in the stomach, we will begin there.