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When you pick up a new prescription, the pharmacist usually covers the basics: take it with food, watch for an upset stomach, do not double up if you miss a dose. What almost nobody mentions is that a handful of very common medications, taken for months or years, can slowly pull certain nutrient levels down.
That is not a reason to be alarmed, and it is definitely not a reason to stop anything your doctor prescribed. It is a reason to know which medications that deplete vitamins are worth asking about, so you can bring it up at your next appointment instead of finding out the hard way.
Quick answer: The best-documented examples are metformin and long-term acid reducers (proton pump inhibitors and H2 blockers), which can lower vitamin B12, and proton pump inhibitors, which can also lower magnesium. Statins may lower levels of coenzyme Q10, though supplementing is not clearly helpful. If you take any of these long term, ask your prescriber whether periodic testing makes sense for you.
[IMAGE: Pharmacist talking with a customer at a pharmacy counter while holding a prescription bottle | alt: pharmacist explaining medications that deplete vitamins to a customer]
Why Medications That Deplete Vitamins Deserve a Conversation
Most of these effects are slow and quiet. A medication that nudges a nutrient down a little each year will not cause symptoms in the first month, and it may never cause any. But over several years, in someone who was already borderline, it can tip the balance.
The mechanisms vary. Some drugs reduce stomach acid, which your body uses to release vitamin B12 from food. Others affect how nutrients are absorbed in the gut or handled by the kidneys. The practical point is the same: the longer you take the medication, the more it is worth checking in.
One habit makes all of this easier: keep a current list of everything you take, including prescriptions, over-the-counter drugs, and supplements, with the dose and roughly how long you have been taking each one. Bring it to every appointment. It turns a vague worry into a specific question your clinician can answer in a couple of minutes.
Metformin and Vitamin B12
Metformin is one of the most widely prescribed diabetes medications, and it is also the clearest example on this list. In a long-term follow-up of the Diabetes Prevention Program published in the Journal of Clinical Endocrinology and Metabolism, each year of metformin use raised the odds of B12 deficiency by about 13% (odds ratio 1.13). At five years, 19.1% of people taking metformin had low or borderline B12, compared with 9.5% of those taking a placebo.
The study authors concluded that routine B12 testing should be considered for people treated with metformin. A 2017 review in American Family Physician adds that the risk rises after more than four months of use. If you have been on metformin for a while and have never had your B12 checked, that is a simple, reasonable thing to ask about.
Acid Reducers: PPIs and H2 Blockers
Proton pump inhibitors (PPIs) such as omeprazole, and H2 blockers such as famotidine, are used for heartburn and reflux, often for years and often bought over the counter. The same AAFP review notes that B12 deficiency risk rises after more than 12 months of use, which makes sense given how much B12 absorption from food depends on stomach acid.
PPIs have a second known effect. The NIH Office of Dietary Supplements notes that the FDA issued a warning in 2011 that taking PPIs for more than a year can cause low magnesium levels. Magnesium helps your muscles, nerves, and heart rhythm work normally, so this one matters, and your doctor may check your level before or during long-term PPI use. Nuts, seeds, beans, whole grains, and leafy greens are the best food sources.
Statins and Coenzyme Q10
Statins lower cholesterol, and according to Mayo Clinic, people who take them may have lower levels of coenzyme Q10 (CoQ10), a compound the body uses in energy production. CoQ10 is not a vitamin, but it comes up constantly because some people on statins deal with muscle aches.
Here is the honest part: Mayo Clinic says some research suggests CoQ10 might ease statin-related muscle pain, but there is not enough evidence to know for sure. It also notes that CoQ10 might make the blood thinner warfarin work less well. If statin side effects bother you, talk with your prescriber before adding CoQ10, since adjusting the dose or switching statins may help more.
Birth Control Pills and B Vitamins
You may have read that oral contraceptives drain folate and B12. The evidence is more reassuring than that. A 2011 review in Nutrition Reviews concluded that the available data do not support a negative effect of current birth control pills on folate status, and that functional markers of B12 status are not significantly affected.
Vitamin B6 is the possible exception. The same review found that low-dose pills may lower B6 status, although the authors say definitive conclusions still await more research. Chickpeas, fish, poultry, potatoes, and bananas are good everyday sources.
A Special Case: Warfarin and Vitamin K
This one works in the opposite direction. The goal with warfarin is not more vitamin K, it is steady vitamin K. The NIH vitamin K fact sheet explains that people taking warfarin need to keep their vitamin K intake from food and supplements consistent, because sudden changes can raise or lower the drug’s effect. We covered the vitamin K picture in more detail in Do You Need Vitamin K2 With Your D3?.
What to Do If You Take One of These Medications
- Do not stop or change your medication on your own. The benefits of these drugs are usually far larger than the nutrient effects, which are manageable.
- Ask about testing. A B12 test for long-term metformin or acid reducer users, or a magnesium check for long-term PPI users, is a normal request.
- Know the signs. Low B12 can show up as fatigue, pale skin, or numbness and tingling in the hands and feet. Our guide to common symptoms of nutrient deficiencies goes into more detail.
- Tell your pharmacist everything you take. That includes supplements, which can interact with medications too.
- Keep an eye on alcohol. Heavy drinking stacks its own nutrient effects on top, as we explained in Does Alcohol Deplete Vitamins?.
What about a multivitamin? A standard one such as Vitamin100, which provides B12 at 100% of the Daily Value, can help cover everyday gaps. It is not designed to correct a deficiency caused by a medication, though. If your levels come back low, your clinician will recommend the right dose and form for you.
Frequently Asked Questions
Should you take B12 if you take omeprazole?
Not automatically. The risk of low B12 rises mainly after more than a year of acid reducer use, so if you have been taking omeprazole that long, ask your doctor about checking your level. If it is low, they can recommend a dose that fits your situation.
Does metformin lower B12 in everyone?
No. In the Diabetes Prevention Program follow-up, most people on metformin did not have low or borderline B12 at five years, but the rate was roughly double that of the placebo group. That is why periodic testing is suggested rather than blanket supplementation.
Should I take CoQ10 with my statin?
Evidence that CoQ10 relieves statin-related muscle pain is not strong enough to know for sure, according to Mayo Clinic. It can also interact with warfarin. Talk with your prescriber first, especially if you take other heart medications.
Do birth control pills deplete folate?
Current research does not support that. A 2011 review found no clear negative effect of today’s oral contraceptives on folate status, although vitamin B6 may be modestly lower in some users.
The Bottom Line
A few everyday medications can slowly lower certain nutrients, with metformin, long-term acid reducers, and B12 at the top of the list. None of that is a reason to skip your prescription. It is a reason to ask one good question at your next visit: “Should we be checking any nutrient levels while I take this?” Your prescriber and pharmacist are the right people to answer it.
Sources
- Long-term Metformin Use and Vitamin B12 Deficiency in the Diabetes Prevention Program Outcomes Study, Journal of Clinical Endocrinology and Metabolism, 2016
- Vitamin B12 Deficiency: Recognition and Management, American Family Physician, 2017
- Magnesium Fact Sheet for Health Professionals, NIH Office of Dietary Supplements, 2026
- Coenzyme Q10, Mayo Clinic, 2025
- Oral contraceptive use: impact on folate, vitamin B6, and vitamin B12 status, Nutrition Reviews, 2011
- Vitamin K Fact Sheet for Health Professionals, NIH Office of Dietary Supplements, 2021
These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease. This article is for general education and is not a substitute for advice from your healthcare provider.