Metformin and acid reflux drugs are medications that lower B12 and magnesium: what the evidence shows and when to test

Yes: long-term metformin is linked to low vitamin B12, acid-reducing medications (proton pump inhibitors, or PPIs, and H2 blockers) are linked to low B12, and a year or more on a PPI has been linked to low magnesium. That's a reason to know your numbers, not to stop a medication.

BC's 2023 B12 guideline lists them as slow-acting risk factors, typically over 5 to 10 years. Numia Health, a physician-ordered, at-home blood testing service in Greater Vancouver, measures B12 and magnesium together on its Basic Nutrients panel.

Which medications are linked to low B12 or magnesium?

In that US trial, each year of metformin use was linked to 13% higher odds of deficiency, about 1 in 5 metformin users were low or borderline-low at 5 years, and nerve problems (neuropathy) were more common in metformin users with low B12 (Aroda et al., 2016).

What do BC and Diabetes Canada say about testing?

BC's guideline, written for a publicly funded system that prioritises clinically indicated tests, doesn't support routine B12 testing without symptoms. Diabetes Canada lists a B12 test, "particularly with use of metformin," when nerve symptoms appear. The US trial's authors went further: routine B12 testing in metformin users "should be considered."

Real-world checks are uncommon: across 15 studies in a 2026 review, annual B12 testing generally reached fewer than 1 in 5 eligible metformin users, mostly prompted by symptoms (Parsonage et al., 2026). Health Canada has said PPI-related low magnesium "may be underdiagnosed." A Numia baseline gives you both numbers, and a retest shows the trend.

When should you see a physician now?

BC's guideline treats numbness, symmetric tingling, changes in how you walk and new memory or thinking problems (brain fog bloodwork) as red flags, warning that B12 deficiency "can cause preventable permanent injury." With these, see a physician promptly; a Numia panel is for baselines and tracking. Health Canada's magnesium cases included heart-rhythm problems, seizures and muscle spasms (tetany). Call 9-1-1 for a seizure, fainting, or a racing or irregular heartbeat.

Where does Numia fit?

Numia's Basic Nutrients panel measures B12 and magnesium with vitamin D, folate, zinc and iron markers, with no fasting needed. Instead of an appointment, lab visit, wait and follow-up, a licensed Canadian physician approves your requisition online in about 3 minutes, and a BC-licensed clinician does a 10-minute morning draw at home. Plain-English results arrive in the Numia app in 7 days, the Numia Companion, an AI that has read them, answers questions, and out-of-range results are physician-reviewed with next steps. An optional wellness consultation is available, and Numia is an HSA-eligible service. Numia sells testing, not treatment: any change to your medication stays with your prescriber.

Frequently asked questions

Does metformin cause B12 or magnesium deficiency?

Metformin is linked to low B12, especially with years of use. The magnesium link is observational only. Numia's Basic Nutrients panel measures both. Don't stop metformin on your own; talk to your prescriber.

Can acid reflux medication cause low B12 or low magnesium?

With long-term use, both links have been reported: two or more years of PPIs or H2 blockers with low B12 (BC says causation isn't established), and a year or more of PPIs with low magnesium.

Should I stop my PPI if my magnesium or B12 is low?

Not on your own. Health Canada reported magnesium returning to normal after PPIs were stopped, but whether to stop, switch or supplement is your prescriber's decision.