Why can't some people digest protein? A look at maldigestion and intolerance

January 9, 2026 •

2 min read

Approximately 15-20% of the population experiences some form of food intolerance. This sheds light on the complex question of why can't some people digest protein, a problem often rooted in specific enzymatic, immunological, or structural issues within the digestive tract, leading to a host of uncomfortable symptoms.

Quick Summary

Protein maldigestion can stem from various causes, including insufficient stomach acid, low pancreatic enzyme production, small intestinal damage from conditions like celiac disease, or specific protein intolerances and genetic factors.

Key Points

Hypochlorhydria: Low stomach acid hinders the initial denaturation of proteins, causing larger, undigested molecules to pass into the intestines.
Pancreatic Insufficiency: A deficient pancreas lacks the proteases needed to break down protein efficiently in the small intestine, common in cystic fibrosis.
Intestinal Damage: Conditions like celiac disease and Crohn's damage the small intestine's lining, reducing surface area for final enzyme action and nutrient absorption.
Food Intolerance vs. Allergy: An intolerance is a non-immune digestive issue (like lactase deficiency with dairy), while an allergy is an immune system reaction to a specific protein.
Genetic Factors: Certain inherited metabolic disorders, such as LPI, directly impact the body's ability to process specific amino acids.
Comprehensive Treatment: Effective management requires addressing the specific root cause, whether through dietary changes, enzyme supplements, or treating an underlying medical condition.

The Complex Process of Protein Digestion

Digesting protein is a multi-step process involving organs and enzymes, starting in the stomach and finishing in the small intestine. Disruptions at any stage can cause digestive issues and malabsorption.

The Stomach's Crucial Role: Denaturation by HCl

Digestion starts in the stomach with gastric juices and hydrochloric acid (HCl), which creates an acidic environment to denature proteins, making them accessible to pepsin. Pepsin breaks proteins into smaller polypeptide chains. Low stomach acid impairs this initial step.

The Small Intestine: Pancreatic and Brush Border Enzymes

Partially digested food moves to the small intestine, where pancreatic enzymes like trypsin and chymotrypsin further break down polypeptides. Brush border enzymes on the intestinal lining complete the breakdown into individual amino acids, which are then absorbed into the bloodstream.

Common Reasons Behind Protein Digestion Problems

Issues affecting protein digestion can lead to symptoms and malabsorption. For more detailed information on common reasons, please visit {Link: Institute for Optimum Nutrition https://ion.ac.uk/articles/low-stomach-acid}.

Comparison of Digestive Issues: Allergy vs. Intolerance vs. Maldigestion


Feature	Food Allergy	Food Intolerance	Maldigestion	Protein Malabsorption
Mechanism	Immune system reaction to a specific protein (e.g., IgE-mediated)	Non-immune system adverse reaction, often due to enzyme deficiency	Failure to chemically break down food into absorbable parts	Failure to absorb nutrients into the bloodstream
Cause	Specific food proteins (e.g., cow's milk, peanuts)	Lack of specific enzyme (e.g., lactase), poor digestion	Low stomach acid (hypochlorhydria), pancreatic issues	Damaged intestinal lining, SIBO, lymphatic issues
Symptoms	Hives, swelling, itching, vomiting, trouble breathing	Bloating, gas, diarrhea, abdominal pain	Bloating, gas, reflux, discomfort, undigested food in stool	Diarrhea, weight loss, fatigue, edema, nutrient deficiencies
Speed of Reaction	Fast, often within minutes to hours	Slower, can be delayed up to 48 hours	Varies, typically during or shortly after meals	Can be a chronic, long-term issue

Symptoms of Impaired Protein Digestion

Issues with protein digestion can manifest in various ways, including gastrointestinal distress like bloating and pain, changes in bowel habits such as chronic diarrhea, and systemic symptoms like fatigue and weight loss. Signs of malnutrition can also occur.

Strategies to Improve Protein Digestion

Improving protein digestion often involves lifestyle and dietary changes, ideally after consulting a healthcare professional. Strategies include chewing food thoroughly, eating smaller meals, staying hydrated, incorporating probiotics, considering digestive enzyme supplements, reducing stress, and managing underlying conditions.

Conclusion: Taking Control of Your Digestive Health

Understanding why some people struggle to digest protein, whether due to low stomach acid, enzyme issues, intestinal damage, or intolerance, is key to finding relief. Consulting a healthcare provider for diagnosis and a personalized plan is crucial for managing these issues and preventing long-term health complications like malnutrition.

For more comprehensive medical information on malabsorption syndromes, visit the {Link: NCBI Bookshelf https://www.ncbi.nlm.nih.gov/books/NBK553106/}.

Frequently Asked Questions

Initial signs of protein digestion issues often include bloating, gas, stomach pain, and general discomfort after eating high-protein foods. Chronic issues can lead to fatigue, weight loss, and changes in stool consistency, such as greasy or fatty stools.

Yes, low stomach acid (hypochlorhydria) is a significant cause of protein maldigestion. The stomach's acidic environment is crucial for denaturing proteins and activating the enzyme pepsin, both vital first steps in the digestive process.

The pancreas releases powerful digestive enzymes called proteases (like trypsin and chymotrypsin) into the small intestine. These enzymes break down protein fragments into smaller peptides and amino acids for absorption.

In celiac disease, consuming gluten triggers an autoimmune response that damages the small intestine lining, specifically the villi where brush border enzymes are located. This reduces the surface area for nutrient absorption, including the final breakdown of protein.

No, they are different. A protein intolerance is an adverse non-immune reaction to a specific protein, while protein malabsorption is the body's inability to break down and absorb the nutrients from protein. A malabsorption issue can be caused by an intolerance, but they are not identical.

Yes, rare genetic conditions can impair protein digestion. Examples include cystic fibrosis, which affects pancreatic enzyme delivery, and lysinuric protein intolerance, which interferes with the body's ability to process certain amino acids.

To improve protein digestion, you can chew food thoroughly, eat smaller meals, stay hydrated, manage stress, and incorporate probiotics or fermented foods. In some cases, a healthcare provider might recommend digestive enzyme supplements.

Diagnosis can involve a series of tests, including blood tests to check for nutrient deficiencies, stool analysis to measure fat or enzyme levels, breath tests for bacterial overgrowth, or endoscopic procedures with biopsies to check for intestinal damage.