Pantoprazole and Magnesium, Vitamin D & B12: What Acid Blockers Do to Your Nutrients

Proton pump inhibitors (PPIs) are among the most frequently prescribed medications. They reduce the production of stomach acid and thereby protect, for example, the oesophagus or the stomach lining.

This article was prompted by two videos: physician Dr. Petra Bracht talks in a YouTube video about medications she views critically, and pharmacist Uwe Gröber explains in a video which nutrients he keeps an eye on with metformin and acid blockers. We checked their statements against studies. You will find the sources at the end of the article.

Stomach acid is involved in digestion. Among other things, it releases vitamin B12 from food proteins so that it can later be absorbed in the small intestine. If acid is strongly reduced over a long period, less B12 may be absorbed.

Vitamin B12: In a case-control study of more than 25,000 people with B12 deficiency, taking acid blockers for two years or longer was associated with a higher risk of deficiency; higher daily amounts more strongly than lower ones (Lam et al., JAMA 2013). A 2023 meta-analysis reached a similar result.

Magnesium: With long-term PPI use, the gut may absorb less magnesium. In 2011 the FDA pointed out that low magnesium levels can occur, mainly after more than one year of use. Meta-analyses of observational studies show an increased risk of low magnesium levels; how often this actually happens has not been conclusively established.

Calcium and bones: Acid blockers can reduce the absorption of calcium carbonate. In observational studies, long-term use was associated with a slightly higher risk of fractures. That is not proof of cause and effect.

This applies to the whole drug class – including omeprazole, esomeprazole, lansoprazole and rabeprazole, not only pantoprazole.

Metformin is a standard medication for type 2 diabetes. That it can lower vitamin B12 levels with long-term use is well documented: in a randomised trial lasting just over four years, B12 fell more with metformin than with placebo (de Jager et al., BMJ 2010), and in the Diabetes Prevention Program long-term use was associated with B12 deficiency (Aroda et al., 2016). Both papers suggest measuring B12 regularly during long-term treatment. One proposed explanation is that metformin impairs the calcium-dependent absorption of B12 in the small intestine.

In his video, Uwe Gröber also mentions vitamin B1, folic acid, magnesium and vitamin D. For these nutrients the evidence is considerably thinner than for B12.

Statins lower cholesterol by inhibiting a metabolic pathway that the body also uses to produce coenzyme Q10. A meta-analysis of placebo-controlled trials shows that blood Q10 levels fall on statins (Banach et al., 2015). Whether Q10 supplementation relieves statin-related muscle symptoms is inconsistent: some meta-analyses find an effect, others do not.

Vitamin B12 deficiency usually develops slowly. Possible signs include tiredness, anaemia, tingling or numbness in the hands and feet, and problems with concentration and memory. Because these complaints can have many causes, they are rarely linked to a stomach medication or to metformin.

Low magnesium can show up as muscle cramps, tremor or heart rhythm disturbances, but often goes unnoticed for a long time. The FDA points to a higher risk especially when other medications that also affect magnesium balance are taken, such as certain diuretics.

A 2025 review describes metformin-related B12 deficiency as an underestimated cause of nerve complaints in diabetes that is easily mistaken for diabetic neuropathy.

None of these signs proves a deficiency. Only a measurement provides clarity.

A 2025 systematic review of older adults taking many medications consistently found lower vitamin B12 and calcium levels with long-term PPI use; for magnesium the results were contradictory.

On coenzyme Q10 with statins, a 2025 meta-analysis found less muscle pain with Q10 in four of seven trials and no difference in three. The authors consider further research necessary.

Most of the data come from observational studies. They show associations, but not that everyone who takes such a medication will develop a deficiency.

If you take acid blockers, metformin or statins over a long period, you can discuss with your treating doctor whether individual values should be measured. Before you take supplements, it is worth looking at the actual value.

• Vitamin B12: Besides the serum B12 level, there are holotranscobalamin and methylmalonic acid, which often indicate an emerging deficiency earlier. Your doctor's practice measures these two.
• Magnesium and other minerals: Serum shows only a small part of the body's stores. The whole blood mineral analysis measures magnesium, zinc, calcium and iron, among others, in whole blood.
• Vitamin B12, folic acid, vitamin D and Q10: The Vitamin Check Basic measures these values from capillary blood. The vitamin D test measures vitamin D only.
• Broader profile: The OM Vital blood test combines blood lipids, liver and kidney values with B12, vitamin D and Q10.

A test does not make a diagnosis. Do not stop a prescribed medication without talking to your doctor first.

With ORY tests, you take the blood sample at home with a finger prick and send it to a partner laboratory in Germany. You receive the results with the laboratory's reference ranges; a results consultation is included.

What a value means for you and whether anything needs to be done is something to discuss with the ORY expert team or with your doctor or naturopath (Heilpraktiker). Bring your list of medications with you.

Studies (all verified via PubMed) and further sources:

1. Lam JR et al. (2013): Proton pump inhibitor and histamine 2 receptor antagonist use and vitamin B12 deficiency. JAMA. PMID 24327038. https://pubmed.ncbi.nlm.nih.gov/24327038/
2. Choudhury A et al. (2023): Vitamin B12 deficiency and use of proton pump inhibitors: a systematic review and meta-analysis. Expert Rev Gastroenterol Hepatol. PMID 37060552. https://pubmed.ncbi.nlm.nih.gov/37060552/
3. Shahid MS et al. (2025): A Systematic Review of Long-Term Use of Proton Pump Inhibitors (PPIs) in Older Adults on Polypharmacy: Do PPIs Deplete Nutrients? Cureus. PMID 40995253. https://pubmed.ncbi.nlm.nih.gov/40995253/
4. Park CH et al. (2014): The association between the use of proton pump inhibitors and the risk of hypomagnesemia: a systematic review and meta-analysis. PLoS One. PMID 25394217. https://pubmed.ncbi.nlm.nih.gov/25394217/
5. Cheungpasitporn W et al. (2015): Proton pump inhibitors linked to hypomagnesemia: a systematic review and meta-analysis of observational studies. Ren Fail. PMID 26108134. https://pubmed.ncbi.nlm.nih.gov/26108134/
6. Srinutta T et al. (2019): Proton pump inhibitors and hypomagnesemia: A meta-analysis of observational studies. Medicine (Baltimore). PMID 31689852. https://pubmed.ncbi.nlm.nih.gov/31689852/
7. O'Connell MB et al. (2005): Effects of proton pump inhibitors on calcium carbonate absorption in women: a randomized crossover trial. Am J Med. PMID 15989913. https://pubmed.ncbi.nlm.nih.gov/15989913/
8. Yang YX et al. (2006): Long-term proton pump inhibitor therapy and risk of hip fracture. JAMA. PMID 17190895. https://pubmed.ncbi.nlm.nih.gov/17190895/
9. da Maia TF et al. (2022): Increased Risk of Fractures and Use of Proton Pump Inhibitors in Menopausal Women: A Systematic Review and Meta-Analysis. Int J Environ Res Public Health. PMID 36294082. https://pubmed.ncbi.nlm.nih.gov/36294082/
10. de Jager J et al. (2010): Long term treatment with metformin in patients with type 2 diabetes and risk of vitamin B-12 deficiency: randomised placebo controlled trial. BMJ. PMID 20488910. https://pubmed.ncbi.nlm.nih.gov/20488910/
11. Aroda VR et al. (2016): Long-term Metformin Use and Vitamin B12 Deficiency in the Diabetes Prevention Program Outcomes Study. J Clin Endocrinol Metab. PMID 26900641. https://pubmed.ncbi.nlm.nih.gov/26900641/
12. Atkinson M et al. (2024): Metformin Use and Vitamin B12 Deficiency in People with Type 2 Diabetes. What Are the Risk Factors? A Mini-systematic Review. touchREV Endocrinol. PMID 39526048. https://pubmed.ncbi.nlm.nih.gov/39526048/
13. (2025): Metformin-induced vitamin B12 deficiency: An underdiagnosed cause of diabetic neuropathy. World J Diabetes. PMID 40697600. https://pubmed.ncbi.nlm.nih.gov/40697600/
14. Banach M et al. (2015): Statin therapy and plasma coenzyme Q10 concentrations – A systematic review and meta-analysis of placebo-controlled trials. Pharmacol Res. PMID 26192349. https://pubmed.ncbi.nlm.nih.gov/26192349/
15. Banach M et al. (2015): Effects of coenzyme Q10 on statin-induced myopathy: a meta-analysis of randomized controlled trials. Mayo Clin Proc. PMID 25440725. https://pubmed.ncbi.nlm.nih.gov/25440725/
16. Qu H et al. (2018): Effects of Coenzyme Q10 on Statin-Induced Myopathy: An Updated Meta-Analysis of Randomized Controlled Trials. J Am Heart Assoc. PMID 30371340. https://pubmed.ncbi.nlm.nih.gov/30371340/
17. Kovacic S et al. (2025): Effects of coenzyme Q10 supplementation on myopathy in statin-treated patients: a systematic review and meta-analysis. J Nutr Sci. PMID 41158831. https://pubmed.ncbi.nlm.nih.gov/41158831/
18. U.S. Food and Drug Administration (2 March 2011): FDA Drug Safety Communication: Low magnesium levels can be associated with long-term use of Proton Pump Inhibitor drugs (PPIs).
19. Thieme: "Protonenpumpenhemmer (PPI): Mikronährstoff-Räuber mit weitreichenden Konsequenzen" (German). https://www.thieme-connect.com/products/ejournals/abstract/10.1055/a-1743-6980
20. Dr. Petra Bracht (2025): "Diese Medikamente meide ich als Ärztin! (Vorsicht!)" YouTube (German). https://www.youtube.com/watch?v=cx6X82GAxjw
21. Uwe Gröber (2022): "Wichtig bei Metformin und Säureblocker: Vitamin B12, B1, Folsäure, Magnesium, Vitamin D." YouTube (German). https://www.youtube.com/watch?v=eI3dshG8MlY
22. Gröber, Uwe (2018): Arzneimittel und Mikronährstoffe – Medikationsorientierte Supplementierung. 4th edition. Stuttgart: Deutscher Apotheker Verlag.

No direct interaction between pantoprazole and magnesium is known. A different link is known: with long-term use of proton pump inhibitors, usually more than a year, the body may absorb less magnesium and levels can fall. The FDA pointed this out in 2011; several meta-analyses confirm an increased risk. Whether you should supplement magnesium is something to clarify with your doctor after a measurement. Whether a particular product should be taken at a different time from other medications is something your pharmacy can answer based on the package leaflets.

No direct interaction between pantoprazole and vitamin D3 is known. An indirect link via calcium is discussed: acid blockers can reduce the absorption of calcium carbonate, and long-term use was associated with a slightly higher risk of fractures in observational studies. If your product contains calcium as well as vitamin D3, ask your pharmacy whether the form of calcium and the timing suit you. A measurement shows where your vitamin D level stands.

It can contribute, but not in everyone. Meta-analyses of observational studies show an increased risk of low magnesium levels with PPI use; a 2025 review in older adults, by contrast, found contradictory results. The FDA points to a higher risk mainly after more than one year of use and when other medications that also affect magnesium balance are taken. It advised doctors to consider measuring magnesium levels in such cases.

In food, vitamin B12 is bound to protein and released with the help of stomach acid. If an acid blocker lowers acid over a long period, less B12 may be absorbed. In a large study, use for two years or longer was associated with a higher risk of B12 deficiency, higher daily amounts more strongly than lower ones (Lam et al., JAMA 2013). A deficiency develops slowly; B12 can be measured in the blood.

Yes. Omeprazole, esomeprazole, pantoprazole, lansoprazole and rabeprazole belong to the same drug class and lower stomach acid in the same way. The FDA notice on magnesium and the large studies on vitamin B12 refer to the whole class. For omeprazole and esomeprazole, too, no direct interaction with magnesium or vitamin D is known. If you want to take omeprazole together with magnesium or vitamin D, the answers above for pantoprazole apply in the same way.

Studies usually refer to long-term use from around one year (magnesium, fractures) or two years (vitamin B12). The daily amount also plays a role: in the study by Lam et al., a higher daily amount was more strongly associated with B12 deficiency than a lower one. Whether you still need your medication at this dose is something you decide together with your doctor. Do not stop a prescribed medication without talking to your doctor first.