Why is my body not absorbing B12 properly?

December 17, 2025 •

4 min read

According to the National Institutes of Health, vitamin B12 malabsorption is the most common cause of B12 deficiency in adults. If you are wondering why is my body not absorbing B12 properly, the answer likely lies in complex digestive processes involving stomach acid and a key protein called intrinsic factor.

Quick Summary

Several factors can cause poor vitamin B12 absorption, including autoimmune conditions like pernicious anemia, digestive diseases, weight-loss surgery, medications, and age-related changes. Diagnosis and treatment often involve medical evaluation and alternative B12 delivery methods.

Key Points

Pernicious Anemia: An autoimmune condition is a major cause of malabsorption, where the body attacks the intrinsic factor required for B12 absorption.
Gut Health Matters: Chronic digestive conditions, bacterial overgrowth, and surgery on the stomach or intestine can all disrupt the B12 absorption process.
Medications Can Interfere: Long-term use of certain drugs, including metformin and stomach acid-reducing medications, can impair B12 uptake.
Age is a Factor: Older adults are at a higher risk due to a natural decrease in stomach acid production, which is essential for releasing B12 from food.
Supplements May Need to Change: For those with malabsorption, standard oral supplements may be ineffective. Higher-dose or alternative delivery methods like injections are often required.
Proper Diagnosis is Crucial: Because symptoms can overlap with other conditions, a thorough medical evaluation is necessary to pinpoint the exact cause of poor absorption.

The B12 Absorption Process: A Complex Journey

Vitamin B12 absorption is not a straightforward process. It begins in the stomach, where stomach acid (hydrochloric acid) separates B12 from the food protein it's attached to. The free B12 then binds to a protein called intrinsic factor, which is produced by cells in the stomach lining. This B12-intrinsic factor complex travels to the small intestine, where it is finally absorbed into the bloodstream. Any disruption along this path can hinder proper absorption, leading to a deficiency, even if your diet contains sufficient amounts of the vitamin.

Autoimmune and Genetic Causes

One of the most common reasons your body may not be absorbing B12 is an autoimmune condition called pernicious anemia. In this disorder, the immune system mistakenly attacks and destroys the stomach cells responsible for producing intrinsic factor. Without sufficient intrinsic factor, the body cannot absorb vitamin B12, regardless of how much is consumed. While the term is often used interchangeably with B12 deficiency, pernicious anemia specifically refers to the autoimmune cause. Genetic factors can also play a role, with rare hereditary disorders affecting the transport of B12.

Medical Procedures and Conditions Affecting B12 Absorption

Many conditions and medical treatments can interfere with the body's ability to absorb B12:

Gastric Surgery: Procedures that alter the stomach or remove part of the small intestine, such as gastric bypass for weight loss, significantly impact B12 absorption. Since these surgeries reduce the stomach's capacity to produce intrinsic factor or bypass the part of the intestine where B12 is absorbed, patients require lifelong supplementation, often via injections.
Chronic Digestive Disorders: Conditions that cause inflammation or damage to the digestive tract can impair B12 absorption. Examples include Crohn's disease, celiac disease, and chronic pancreatitis.
Bacterial Overgrowth: An overgrowth of certain bacteria in the small intestine can lead to a B12 deficiency. These bacteria consume the B12 before the body has a chance to absorb it.
Atrophic Gastritis: This condition, which causes chronic inflammation and thinning of the stomach lining, often results in decreased production of stomach acid and intrinsic factor, both vital for B12 absorption. It is more common in older adults and can be caused by Helicobacter pylori infection.

Medications and Lifestyle Factors

Certain medications are known to reduce the absorption of B12 with long-term use. These include:

Metformin: A common diabetes medication.
Proton Pump Inhibitors (PPIs) and H2 Blockers: Medications used to treat heartburn and acid reflux, which reduce stomach acid production.
Antibiotics: Long-term use of certain antibiotics can affect the gut bacteria balance, potentially interfering with B12 absorption.

Lifestyle habits also play a part. Excessive and prolonged alcohol consumption can damage the stomach and intestinal lining, leading to malabsorption of nutrients, including B12. While less common in developed countries, dietary insufficiency—particularly in strict vegans and vegetarians who do not consume fortified foods or supplements—is another potential cause, though true malabsorption is a distinct issue from dietary lack.

Comparison of Causes for Poor B12 Absorption


Cause	Mechanism of Action	Affected Population	Treatment Approach
Pernicious Anemia	Autoimmune attack on intrinsic factor-producing stomach cells.	Individuals, often over 60, with autoimmune history; more common in Northern Europeans and those of African descent.	Injections of B12 (hydroxocobalamin) or high-dose oral supplements.
Gastric/Intestinal Surgery	Removal or alteration of stomach/intestinal sections reduces intrinsic factor and absorption site.	Post-bariatric or other gastric surgery patients.	Lifelong B12 injections or high-dose oral supplements.
Atrophic Gastritis	Inflammation of stomach lining reduces stomach acid and intrinsic factor.	More common in older adults; can be caused by H. pylori infection.	High-dose oral B12 supplements, which don't require stomach acid for absorption.
Medications (e.g., PPIs, Metformin)	Long-term use reduces stomach acid or interferes with B12 uptake.	Patients on long-term treatment for diabetes or acid reflux.	B12 supplementation; consult a doctor about medication alternatives.
Chronic Digestive Diseases	Inflammation or damage to the small intestine (e.g., Crohn's, Celiac) impairs nutrient uptake.	Individuals with specific digestive diagnoses.	Managing the underlying disease and B12 supplementation.

Conclusion

Understanding why your body is not absorbing B12 properly requires a careful look at your medical history, current health, and lifestyle. The issue is rarely a simple lack of B12 in the diet but rather a malfunction in the complex absorption pathway. Identifying the root cause—whether it’s an autoimmune condition like pernicious anemia, a chronic digestive disease, the side effect of a medication, or a consequence of gastric surgery—is the critical first step. With a proper diagnosis from a healthcare provider, an effective treatment plan can be implemented. For those with confirmed malabsorption, oral supplementation may be insufficient, and alternative methods such as injections or high-dose sublingual supplements are often necessary to restore and maintain healthy B12 levels. To read more about specific causes and treatments, the National Heart, Lung, and Blood Institute provides comprehensive information on B12 deficiency anemia.

National Heart, Lung, and Blood Institute Website

Frequently Asked Questions

Intrinsic factor is a protein produced by the stomach lining. Its role is to bind with B12 in the stomach, forming a complex that the small intestine can absorb. Without it, the body cannot effectively absorb B12 from food.

Yes. While a poor diet is one cause of deficiency, the most common reason is an inability to properly absorb the vitamin, which can be caused by underlying medical conditions or issues with the digestive system.

Metformin can interfere with the vitamin's absorption in the intestine. Proton pump inhibitors (PPIs) and H2 blockers reduce stomach acid, which is necessary to release B12 from food proteins, both hindering the process.

No, while it is a frequent cause, many other conditions can lead to poor absorption. These include other autoimmune diseases, celiac disease, Crohn's disease, atrophic gastritis, and having undergone gastric surgery.

Diagnosis typically involves a blood test to check B12 levels. Additional tests may be ordered to measure intrinsic factor antibodies or conduct a gastric evaluation, especially for younger patients or those where the cause isn't clear.

For many malabsorption issues, standard oral supplements are ineffective because they rely on the same faulty absorption process. High-dose oral supplements, however, can be passively absorbed in small amounts. Injections are often the most reliable method for those with severe malabsorption.

Prevention depends on the cause. For dietary deficiencies, consuming fortified foods or supplements is key. For those with underlying medical conditions, managing the disease is critical. For instance, vegans must supplement, and those with gastric issues may require monitored treatment.