What is the end product of protein digestion? Quick Answer. Mansoura University explains that the end products of protein digestion in the small intestine are amino acids. The amino acids are then absorbed into the bloodstream through the walls of the intestine with the help of carrier proteins or other mechanisms. This digestion is at the end of a multi-step process during which the proteins are denatured and progressively broken into their constituent peptides by a sequence of enzymes.