How Is Protein Absorbed by the Digestive Tract?

Protein is digested in your stomach and absorbed in your small intestine.

Protein is digested in your stomach and absorbed in your small intestine.

Dietary protein is not just important for building big muscles, it’s also needed for the growth and repair of skin, hair and fingernails, as well as for making enzymes. Before protein is absorbed in the digestive tract, it’s metabolized or broken down into smaller building blocks called amino acids. The amino acids are then transported in your blood to be used as building material for the proteins in your body.


Animal and plant proteins are made from long chains called polypeptides. These long chains need to be broken into individual amino acids before dietary protein becomes useful for your body. During adulthood, your body uses 22 different amino acids to build and repair its protein-based structures. If dietary protein is absorbed before it’s broken down, as can be the case with some intestinal diseases such as leaky gut syndrome, your immune system will attack it as if it’s a foreign invader. Absorbed undigested protein can get lodged within joints, glands and organs and trigger inflammatory reactions that are sometimes misdiagnosed as auto-immune disease.


Chewing on protein in your mouth starts the mechanical breakdown of food, but the chemical digestion of polypeptides doesn’t happen until food enters your stomach. Once in your stomach, gastric acid starts to unfold the protein molecules and an enzyme called pepsin begins to metabolize the polypeptides into smaller peptide fragments and amino acid clumps. After about four hours of churning, the partially digested protein material exits your stomach and enters your small intestine where it comes in contact with different enzymes. Your pancreas releases special proteases such as trypsin and chymotrypsin into the small intestine, which finish reducing the peptide fragments into individual amino acids.


In a healthy and normally functioning digestive tract, only the amino acids from protein digestion are absorbed through the walls of the small intestine. More specifically, small folds called intestinal villi are where amino acids and other nutrients pass through the intestine and into your bloodstream. The initial part of your small intestine, called the duodenum, is where the final digestion of protein takes place, but it’s the middle and end segments of the small intestine, called the ileum and jejunum, respectively, where amino acid absorption occurs. The total time needed for protein digestion and complete absorption ranges from about one to three days, depending on your metabolic rate and intestinal motility.

Protein for Energy

Amino acids are typically used as building blocks, but if you don’t eat enough carbohydrates or fats, then your body can use amino acids for energy. Your body will metabolize protein from your muscles and other tissues back into amino acids and then covert them into glucose for use as energy in extreme situations, but only if all your fat reserves are depleted.



  • Textbook of Functional Medicine; David S. Jones
  • Human Biochemistry; Charles Dreiling
  • Human Metabolism: Functional Diversity and Integration; J. Ramsey Bronk

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