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Pantoprazole Magnesium: Low Magnesium Risks & Benefits

Article on how pantoprozole can lead to low magnesium

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Pantoprazole magnesium is a prescription medication used for the management of certain gastroesophageal conditions that are caused by too much acid in the stomach.

This medication, like Omeprazole, belongs to a class of drugs called proton pump inhibitors (PPIs). PPIs shut down pumps in the stomach that produce extra stomach acid, reducing painful symptoms in your stomach and esophagus. 

Pantoprazole magnesium is available as the prescription brand name Protonix and in generic form.

In this post, we will explore the benefits of taking pantoprazole, the potential side effects of PPIs and pantoprazole, and the relationship between magnesium levels and this common prescription medication.

The Potential Benefits of Pantoprazole Magnesium

Pantoprazole magnesium is used to treat acid reflux, heartburn, and gastroesophageal reflux disease (GERD). Doctors also prescribe it to prevent and treat stomach ulcers. In some cases, it is used to treat a rare condition in the gut called Zollinger-Ellison syndrome that is caused by a tumor in the pancreas or the gut.

Side Effects of Pantoprazole Magnesium

Common side effects of pantoprazole include:

  • Stomach pain
  • Nausea or vomiting
  • Gas
  • Headache
  • Joint pain
  • Diarrhea
  • Dizziness
  • Joint pain

If you have any of these more serious side effects, call your doctor or 911 right away:

  • Severe diarrhea: Health Canada issued a warning of a possible association between taking proton pump inhibitors like pantoprazole and an increased risk of Clostridium difficile-associated diarrhea (also known as CDAD or C. difficile). Symptoms of CDAD can include diarrhea, stomach pain, or a fever that doesn’t resolve. Risk factors that can increase the risk of infection are underlying illnesses, hospitalization, antibiotic use, and advanced age.
  • Cutaneous lupus erythematosus (CLE): Symptoms can include weight loss, fatigue, a rash across the cheeks, or red scaly areas of skin on your body.
  • Bone fractures: Long-term use of PPIs has been linked with an increased risk for fractures of the spine, hip, and wrist.
  • Kidney damage: If you experience changes in urination or you have pain in your sides and back, see your doctor immediately.

Pantoprazole Magnesium and Deficiency of Vitamins and Minerals

Taking this drug for longer than three years can make it harder for your system to absorb vitamin B-12. Symptoms of low B-12 include numbness or tingling in the hands or feet, poor muscle coordination, nervousness, neuritis, and changes in menstruation. 

Taking pantoprazole for three months or more can also lead to low magnesium levels (hypomagnesemia). This may seem counterintuitive because of the name of the drug, “pantoprazole magnesium”. However, pantoprazole contains very little of the mineral magnesium, yet appears to deplete your body’s magnesium stores.

The symptoms of low magnesium levels include:

  • Tremors
  • Seizures
  • Jitteriness
  • Muscle weakness
  • Fast heart rate
  • Dizziness
  • Muscle aches or cramps
  • Voice box spasms

(Learn more about signs of low magnesium here.)

In a study published in Gastroenterology Report in August 2014, researchers found a connection between proton pump inhibitors and hypomagnesemia. 

“In our case series pantoprazole (lowest potency for acid suppression) caused hypomagnesaemia in 2 of 4 patients and esomeprazole in 2 of 4 patients. Thus there is a class effect in PPIH that is not completely explained by PPI potency alone.”

If you discover that you are low on magnesium while taking pantoprazole, talk to your doctor about the possibility of supplementing your diet with magnesium citrate to increase your levels.

Pantoprazole, Low Stomach Acid, and Magnesium

Proton pump inhibitors are supposed to decrease acid in your stomach – thus leading to relief of the symptoms of stomach ulcers, heartburn, and GERD – but some experts believe that digestive issues are caused by too little stomach acid.

In her book The Magnesium Miracle, Dr. Carolyn Dean, M.D., N.D., says:

“Heartburn and indigestion, the result of bad eating habits, plague the nation. But the ‘cure’ in this case is no better than the disease. The roiling and burning in the gut from sugary junk food and greasy fast food is being inappropriately blamed on too much stomach acid. In many cases, heartburn is due to sugar fermentation in the stomach and a backflow of pancreatic enzymes from the small intestine.”

– Dr. Carolyn Dean

There is a close relationship between magnesium and digestive issues. We need magnesium to regulate the amount of stomach acid we produce. When proton pump inhibitors neutralize our normal stomach acids, it cuts down on our ability to absorb magnesium – therefore leading to more problems with our stomach acids!

Getting Relief From Digestive Symptoms with Magnesium Citrate

Natural Calm® Magnesium for Constipation

If you are struggling with acid reflux, heartburn, or other stomach issues associated with GERD, you may benefit from adding a magnesium citrate supplement to your diet. Magnesium citrate enhances digestion because it includes the acid some people are missing. Talk to your doctor about whether taking magnesium citrate might be helpful for you, particularly if you are taking pantoprazole magnesium or any other prescription medication.

You can take magnesium in small doses during the day, instead of all at one time. Splitting up your dose of magnesium gives your body additional time to absorb the mineral and prevents diarrhea that may occur from taking too much at one time

Natural Calm® magnesium citrate powder is gentle, easily-absorbable magnesium that is appropriate for people with digestive issues. You can sip Natural Calm throughout the day if you want, or drink your full dose in the morning or evening, depending on how your symptoms respond.


  • “Recalls and Safety Alerts.”, 2013, Accessed 31 May 2023.
  • Wang, Liwei, et al. Proton Pump Inhibitors and the Risk for Fracture at Specific Sites: Data Mining of the FDA Adverse Event Reporting System. no. 1, July 2017, Accessed 31 May 2023.
  • Wei, James, et al. Hypomagnesaemia Associated with Long-Term Use of Proton Pump Inhibitors. no. 3, Aug. 2015, pp. 243–53, Accessed 31 May 2023.
  • “Welcome – Dr Carolyn Dean MD ND.” Dr Carolyn Dean MD ND, 13 Mar. 2023, Accessed 31 May 2023.

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