Nutrients Depleted By Proton Pump Inhibitors

A woman holds her stomach in discomfort.

When stomach acid production is impeded by proton pump inhibitors, it can lead to reduced digestion and absorption of nutrients.

Proton Pump Inhibitors (PPIs) are a widely prescribed class of medications known for their effectiveness in reducing stomach acid production. While they can provide relief from the discomfort associated with excessive stomach acid, many people may not be aware that PPIs can have a significant impact on our nutritional well-being (1). 

In this article, we'll explore which nutrients can be depleted by proton pump inhibitors, why the depletions occur, and how to counteract their effects.

Why Are Proton Pump Inhibitors Prescribed?

These drugs are often used to manage conditions such as gastroesophageal reflux disease (GERD), peptic ulcers, long term NSAID use, and gastritis. PPIs inhibit the action of proton pumps in the stomach lining, ultimately decreasing the secretion of gastric acid. Some well-known PPIs include Omeprazole (Prilosec), Esomeprazole (Nexium), and Lansoprazole (Prevacid).

How Do Proton Pump Inhibitors Affect Nutrient Status?

To comprehend how PPIs influence nutrient levels in the body, we must understand their mechanism of action. These drugs effectively reduce stomach acid, which plays a crucial role in breaking down food and aiding in the absorption of nutrients (2). When stomach acid production is impeded by proton pump inhibitors, it can lead to reduced digestion and absorption of certain nutrients, particularly those that require an acidic environment for proper assimilation (3).

Key Nutrients Depleted by Proton Pump Inhibitors

Proton pump inhibitors are known to deplete several essential nutrients in the body, including the following: 


Calcium relies on stomach acid for absorption. Inadequate calcium absorption can potentially lead to bone health issues, including osteoporosis (4). Studies show that infant use of PPIs can increase fracture risk later in life (5).


Reduced stomach acid can hinder the absorption of dietary iron, increasing the risk of iron deficiency and anemia (6).


PPIs can lead to magnesium deficiencies, affecting muscle and nerve function, blood glucose control, and blood pressure regulation. About half of the US population is estimated to be deficient in magnesium (7) and the use of PPIs are associated with hypomagnesemia - an electrolyte disturbance caused by a low serum magnesium level (8). 

A fatigued woman rests at her desk.

Vitamin B12 

The absorption of vitamin B12 is also compromised by the use of PPIs (1). This vitamin is vital for various physiological processes, including DNA synthesis and nerve function. A B12 deficiency can lead to fatigue, anemia, and neurological issues (9).

How To Maintain Nutritional Balance While Taking Proton Pump Inhibitors

Though proton pump inhibitors affect the absorption of certain nutrients, they do not bring absorption to a complete halt. To enhance nutrient absorption, look for nutrient sources that are easily absorbed or don’t require the presence of acid for digestion. You may also take supplements that improve the breakdown of food, such as digestive enzymes. 

Tips for optimizing nutrient absorption:

  1. Use sublingual B12 supplements like Methyl Factors - sublingual absorption bypasses the need for gastric acid.

  2. Look for easily broken apart mineral chelates like bisglycinates, glycinates, and citrates. All the Dr. Green Life minerals are in forms that are easy to digest for optimal absorption and to reduce digestive discomfort. 

  3. Combine iron rich foods or iron supplements with vitamin C to enhance absorption.

  4. Consume cooked foods, which are partially broken down during the cooking process. 

  5. Focus on nutrient-rich foods.


Proton Pump Inhibitors are a tool used by many to help manage gastrointestinal conditions, but their impact on nutrient levels in the body should not be overlooked. The resulting decrease in stomach acid may mean that less nutrients are absorbed from food. Nutrients that can be depleted by PPIs include calcium, iron, magnesium, and vitamin B12. GERD is a condition that can be treated favorably through natural measures, but for individuals who are using PPIs, a proactive approach involves a diet rich in essential nutrients and, in many instances, nutrient supplementation.


  1. Heidelbaugh J. J. (2013). Proton pump inhibitors and risk of vitamin and mineral deficiency: evidence and clinical implications. Therapeutic advances in drug safety, 4(3), 125–133.

  2. NCBI. (2016, August 21). How does the stomach work?; Institute for Quality and Efficiency in Health Care (IQWiG).

  3. Freedberg, D. E., Lebwohl, B., & Abrams, J. A. (2014). The impact of proton pump inhibitors on the human gastrointestinal microbiome. Clinics in laboratory medicine, 34(4), 771–785.

  4. Cleveland Clinic. (2011). Osteoporosis Prevention With Calcium Treatment | Cleveland Clinic. Cleveland Clinic.

  5. Thong, B. K. S., Ima-Nirwana, S., & Chin, K. Y. (2019). Proton Pump Inhibitors and Fracture Risk: A Review of Current Evidence and Mechanisms Involved. International journal of environmental research and public health, 16(9), 1571.

  6. Iron-Deficiency Anemia. (2020, July 20).

  7. ‌Low magnesium levels make vitamin D ineffective. (n.d.). ScienceDaily. Retrieved November 20, 2023, from

  8. Srinutta, T., Chewcharat, A., Takkavatakarn, K., Praditpornsilpa, K., Eiam-Ong, S., Jaber, B. L., & Susantitaphong, P. (2019). Proton pump inhibitors and hypomagnesemia. Medicine, 98(44), e17788.

  9. ‌Ankar A, Kumar A. Vitamin B12 Deficiency. [Updated 2022 Oct 22]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from:

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