What Causes Poor Absorption of B Vitamins?

November 18, 2025 •

4 min read

While 80-90% of vitamin B12 in supplements is consumed by bacteria in the human gut, various other factors prevent the body from properly absorbing B vitamins from both food and supplements. This critical nuance is why simply eating fortified foods or taking a vitamin may not always solve a deficiency, and understanding what causes poor absorption of B vitamins is essential for effective treatment.

Quick Summary

Several medical conditions like pernicious anemia, chronic diseases, and gastrointestinal surgeries can impair B vitamin uptake. Additionally, certain medications, excessive alcohol consumption, and aging can contribute to poor absorption, leading to potential deficiencies and health complications.

Key Points

Pernicious Anemia: An autoimmune disease that eliminates intrinsic factor, causing B12 malabsorption from food.
Reduced Stomach Acid: Conditions like atrophic gastritis and use of PPIs can hinder the release of B12 from food proteins.
GI Disorders: Celiac disease, Crohn's disease, and SIBO damage the intestines and interfere with the absorption of B vitamins.
Medication Side Effects: Long-term use of medications like metformin and acid-blockers can cause or worsen poor B vitamin absorption.
Age and Lifestyle: The aging process and excessive alcohol consumption are significant factors that can negatively impact the body’s ability to absorb B vitamins.
Surgical Impact: Gastric and intestinal surgeries, including weight-loss procedures, can reduce the area available for B vitamin absorption.

How the Absorption of B Vitamins Works

B vitamins are a group of water-soluble nutrients that the body cannot store in significant amounts (with the exception of B12 and folate, which are stored in the liver). This means a regular supply is needed through diet. The absorption process, particularly for vitamin B12, is complex and depends heavily on the proper function of the stomach and small intestine. Digestion begins in the stomach, where stomach acid and pepsin release B12 from the food proteins it's attached to. It then binds to a protein called intrinsic factor, which is essential for its absorption in the ileum (the last part of the small intestine). Most other B vitamins are absorbed through different mechanisms, but are still reliant on a healthy digestive system.

Medical Conditions Impairing B Vitamin Absorption

Many medical issues can disrupt the delicate process of nutrient absorption, leading to B vitamin deficiencies even when dietary intake is adequate. These include:

Pernicious Anemia: An autoimmune condition where the body attacks the stomach cells that produce intrinsic factor, making B12 absorption impossible through food. Sufferers require regular B12 injections.
Atrophic Gastritis: A condition causing chronic inflammation and thinning of the stomach lining, which reduces the production of stomach acid and intrinsic factor. This is a common cause of B12 malabsorption, especially in older adults.
Gastrointestinal Disorders: Diseases affecting the intestines directly impede nutrient uptake. These include inflammatory bowel diseases (IBD) like Crohn’s disease and ulcerative colitis, as well as celiac disease. Crohn's disease can be particularly impactful if it affects the ileum where B12 is absorbed.
Small Intestinal Bacterial Overgrowth (SIBO): An overgrowth of bacteria in the small intestine can consume B vitamins before the body has a chance to absorb them, leading to deficiency.
H. pylori Infection: Chronic infection with Helicobacter pylori is linked to atrophic gastritis and reduced B12 absorption.
Pancreatic Insufficiency: The pancreas produces enzymes necessary for freeing B vitamins from their binding proteins. Insufficiency can therefore compromise absorption.
Intestinal Parasites: The fish tapeworm, Diphyllobothrium latum, can compete with the host for vitamin B12, causing a deficiency.

Medications and Surgeries Affecting Absorption

Certain Drugs Can Block Absorption

Proton Pump Inhibitors (PPIs) and H2-Receptor Antagonists: Used for acid reflux and peptic ulcers, these medications reduce stomach acid. Lower stomach acid impairs the release of B12 from food, hindering absorption.
Metformin: A common diabetes medication, its long-term use is associated with reduced B12 absorption. This is thought to be due to altered calcium homeostasis in the ileum.
Certain Antibiotics and Anti-seizure Medications: Drugs like chloramphenicol and some antiepileptics may also interfere with B12 absorption.

Gastric and Intestinal Surgeries

Any surgical procedure that alters the stomach or intestinal tract can have a profound impact on B vitamin absorption. Gastric bypass surgery, for example, alters the path of digestion, bypassing the parts of the stomach and small intestine responsible for producing intrinsic factor and absorbing B12. The removal of parts of the stomach or ileum can have similar effects.

Lifestyle and Other Factors

Alcohol Consumption

Excessive alcohol use can damage the stomach lining, leading to gastritis and reduced stomach acid, which hinders B vitamin absorption, especially B12 and folate. It can also increase the body's excretion of some B vitamins.

Dietary Considerations

Vegans and vegetarians are at higher risk for B12 deficiency since it is naturally found almost exclusively in animal products. While fortified foods and supplements are available, individuals must ensure consistent intake.

The Role of Age

Aging naturally leads to a decrease in stomach acid production (atrophic gastritis), which is a common cause of poor B12 absorption in older adults. The incidence of pernicious anemia also increases with age.

Factors Affecting B12 Absorption vs. Other B Vitamins


Factor	Vitamin B12 Absorption	Other B Vitamin Absorption (e.g., B1, B2, B6)
Mechanism Dependency	Highly dependent on intrinsic factor and stomach acid for release from food.	Relies on passive diffusion and/or specific carrier-mediated transport systems.
Intrinsic Factor Lack	Complete or near-complete failure of food-bound B12 absorption, as seen in pernicious anemia.	Does not directly affect absorption.
Stomach Acid Reduction	Significantly reduced absorption of B12 from food. Less impact on B12 from supplements.	Minimal direct impact, though extreme changes in pH can influence some absorption.
Site of Absorption	Primarily absorbed in the distal ileum.	Absorbed throughout the small and large intestines.
Bacterial Overgrowth	Competing bacteria consume B12, causing malabsorption in SIBO.	Can affect other B vitamins, though some gut bacteria also produce them.

Conclusion: Addressing the Root Cause

Poor absorption of B vitamins is a complex issue with a range of potential causes, from autoimmune diseases and digestive disorders to the effects of medication and lifestyle. Addressing a deficiency requires more than just increasing dietary intake; it necessitates identifying and treating the underlying absorption problem. For conditions like pernicious anemia, this may mean regular injections to bypass the digestive tract entirely. In other cases, managing the underlying disease, adjusting medication, or supplementing with highly bioavailable forms of B vitamins may be effective. Anyone suspecting poor absorption should consult a healthcare provider for proper diagnosis and a personalized treatment plan.

For further reading on B vitamin deficiencies:

Vitamin B12 - Health Professional Fact Sheet

Frequently Asked Questions

The most common cause is a lack of intrinsic factor, a protein required for B12 absorption. This can be due to an autoimmune disease called pernicious anemia or decreased stomach acid, common in older adults.

Yes, long-term use of acid-suppressing medications, such as proton pump inhibitors (PPIs) and H2-receptor antagonists, can significantly lower stomach acid. This makes it harder to release vitamin B12 from food, hindering absorption.

These gastrointestinal diseases cause inflammation and damage to the intestinal lining. This physical damage prevents the body from effectively absorbing nutrients, including B vitamins, through the intestinal wall.

While their primary risk for B12 deficiency is low dietary intake, they are also susceptible to absorption problems like anyone else. Vegans in particular must rely on fortified foods or supplements, as B12 is almost exclusively found in animal products.

Yes, chronic and excessive alcohol use can damage the stomach and intestinal lining, leading to gastritis and malabsorption. It can also interfere with the metabolism and excretion of B vitamins.

As people age, stomach acid production often decreases, a condition known as atrophic gastritis. This reduces the body's ability to free B12 from food and can cause poor absorption, affecting a large percentage of older adults.

Gut bacteria can both produce and consume B vitamins. An imbalance, such as Small Intestinal Bacterial Overgrowth (SIBO), can lead to bacteria consuming vitamins before the host can absorb them. The health of the gut microbiota can therefore significantly impact B vitamin levels.