Can a B12 Deficiency Cause Indigestion? A Look at Gut Health and Vitamin B12

October 13, 2025 •

4 min read

According to research from the NHS, indigestion is one of the many symptoms that can occur with a vitamin B12 deficiency. This critical nutrient plays a vital role in red blood cell formation and neurological function, but its absence can also disrupt the delicate balance of the digestive system. So, can a B12 deficiency cause indigestion? The answer is a clear yes, and the reasons are deeply rooted in how the body processes this essential vitamin.

Quick Summary

A deficiency in vitamin B12 can disrupt proper digestive function by impacting stomach acid production and nerve signaling in the gut, leading to symptoms like indigestion, bloating, and altered bowel movements. Addressing the root cause is necessary for relief.

Key Points

Direct Link: A B12 deficiency can directly cause indigestion and other gastrointestinal symptoms, including bloating, nausea, and changes in bowel habits.
Stomach Acid Role: Proper B12 absorption requires adequate stomach acid; conditions that reduce stomach acid, like gastritis or certain medications, can lead to deficiency.
Anemia's Effect: The anemia resulting from a B12 deficiency can decrease oxygen supply to the digestive tract, further disrupting its normal function.
Neurological Impact: B12 is essential for nerve health, and its deficiency can impair the nerves that control gut motility, leading to constipation or diarrhea.
Pernicious Anemia: An autoimmune condition that prevents intrinsic factor production is a major cause of B12 deficiency and its associated digestive problems.
Treatment is Key: Managing the underlying deficiency, often with injections or high-dose oral supplements, is necessary to resolve both the deficiency and the related indigestion.

The Connection Between Vitamin B12 and Digestion

Vitamin B12, or cobalamin, is crucial for numerous bodily processes, including DNA synthesis and the formation of red blood cells. Its absorption is a complex process that begins in the stomach and involves several key players. A breakdown at any stage can lead to a deficiency and subsequent digestive issues.

The digestive process requires adequate stomach acid (hydrochloric acid) to separate vitamin B12 from the food it's bound to. A protein called intrinsic factor, produced in the stomach, is then needed to bind with the B12, allowing it to be absorbed in the small intestine. If stomach acid or intrinsic factor is lacking, B12 absorption is compromised, leading to deficiency even with sufficient dietary intake.

How B12 Deficiency Leads to Indigestion and Other GI Symptoms

When B12 levels are low, several digestive problems can emerge:

Impact on Red Blood Cells: A lack of B12 can lead to anemia, a condition where the body doesn't have enough healthy red blood cells. Red blood cells are responsible for carrying oxygen throughout the body, including to the digestive tract. Insufficient oxygen can disrupt normal gut function and metabolism, leading to symptoms like nausea and indigestion.
Nerve Damage: Vitamin B12 is essential for maintaining a healthy nervous system. A deficiency can damage the nerves throughout the body, including those that control the digestive tract. This neurological impact can lead to altered gut motility, causing either constipation or diarrhea.
Stomach Lining Inflammation: Conditions like gastritis (inflammation of the stomach lining) can cause or be exacerbated by a B12 deficiency. Atrophic gastritis, in particular, reduces stomach acid and intrinsic factor production, creating a vicious cycle where poor absorption leads to more deficiency.
Gut Microbiome Disruption: Some evidence suggests that vitamin B12 levels can influence the composition of the gut microbiome. An imbalance in gut bacteria may contribute to gastrointestinal symptoms such as gas, bloating, and discomfort.

Medical Conditions Linked to B12 Deficiency

Several medical conditions can directly cause a B12 deficiency and trigger digestive complaints:

Pernicious Anemia: An autoimmune condition where the immune system attacks the stomach cells that produce intrinsic factor. This is a major cause of B12 deficiency, with common symptoms including indigestion, nausea, and bloating.
Gastritis: Chronic inflammation of the stomach lining, which often results in reduced stomach acid production.
Digestive Disorders: Conditions like Crohn's disease and celiac disease can damage the lining of the small intestine, impairing B12 absorption.
Stomach Surgery: Procedures such as gastric bypass can reduce the area of the stomach that produces acid and intrinsic factor, severely limiting B12 absorption.
Use of Acid-Blocking Medications: Long-term use of proton pump inhibitors (PPIs) and H2 receptor antagonists can decrease stomach acid, which is necessary for releasing B12 from food.

How to Manage B12-Related Indigestion

Managing indigestion caused by a B12 deficiency requires addressing the root cause. A healthcare professional can determine the best course of action based on the severity and cause of the deficiency.

Treatment Options:

Vitamin B12 Injections: For severe deficiencies or absorption issues, injections of vitamin B12 (hydroxocobalamin or cyanocobalamin) are the most effective treatment. This bypasses the need for stomach absorption entirely.
Oral Supplements: High-dose oral supplements may be effective for some individuals, particularly those with reduced stomach acid who can still absorb some B12 from supplements.
Dietary Adjustments: Increasing consumption of B12-rich foods is a good preventative measure but may not be enough to correct a significant deficiency, especially if absorption is the main issue.
Addressing Underlying Conditions: Treating any underlying conditions, such as Crohn's or gastritis, is crucial for improving absorption and resolving symptoms.

Comparison: Indigestion from B12 Deficiency vs. General Indigestion


Symptom	Indigestion from B12 Deficiency	General Indigestion (e.g., from diet)
Onset	Gradual, worsening over time	Often acute and linked to specific foods or meals
Associated Symptoms	Fatigue, neurological issues (e.g., tingling), pale skin, smooth/sore tongue, mood changes	Primarily focused on the upper abdomen (heartburn, bloating, burping)
Bowel Movements	Can include diarrhea, constipation, or alternating patterns	Generally less likely to cause extreme changes in bowel habits
Underlying Cause	Impaired absorption due to low stomach acid, lack of intrinsic factor, or other GI diseases	Overeating, eating too quickly, high-fat foods, spicy foods
Duration	Persistent and chronic if left untreated	Typically resolves after a few hours or a day

Conclusion

In summary, there is a clear and well-documented link between vitamin B12 deficiency and indigestion. This is not simply a side effect but a direct result of the vitamin's critical role in both digestive processes and overall neurological health. Addressing indigestion caused by a B12 deficiency requires a proper diagnosis from a healthcare provider to identify the underlying cause, whether it's dietary, autoimmune, or medication-related. By treating the deficiency, not only can digestive symptoms improve, but the broader effects on energy levels, mood, and neurological function can also be resolved.

For more detailed information on vitamin B12 and its effects on the body, refer to the NIH Office of Dietary Supplements website.

Frequently Asked Questions

B12 deficiency can cause a variety of gastrointestinal symptoms, including generalized indigestion, nausea, bloating, and abdominal pain. It can also lead to changes in bowel movements, such as constipation or diarrhea.

Yes, low stomach acid (hypochlorhydria), often caused by conditions like atrophic gastritis or the long-term use of acid-blocking medications, can significantly reduce the body's ability to absorb vitamin B12 from food.

Pernicious anemia is a common cause, especially in older adults, where the body's immune system attacks the cells that produce intrinsic factor, a protein necessary for B12 absorption. This often leads to both B12 deficiency and digestive issues.

Indigestion from a B12 deficiency is often accompanied by other symptoms like fatigue, weakness, pale skin, a sore or smooth tongue, and neurological issues such as tingling or numbness. A doctor can confirm the cause with a blood test.

Vitamin B12 is naturally found in animal products like meat, fish, eggs, and dairy. Fortified cereals and nutritional yeast are good options for vegetarians and vegans.

If poor absorption is the root cause, treatment usually involves B12 injections to bypass the digestive tract. In some cases, high-dose oral supplements can also be effective.

Yes, a B12 deficiency can affect both. It can lead to psychological problems ranging from mild anxiety to depression, while also causing a variety of digestive issues.