The Long-Term Side Effects of Using Proton Pump Inhibitors (PPIs) for GERD


If you’ve ever struggled with heartburn, acid reflux, or GERD (Gastroesophageal Reflux Disease), chances are you’ve been prescribed—or recommended—proton pump inhibitors (PPIs). Medications like omeprazole (Prilosec), esomeprazole (Nexium), or pantoprazole (Protonix) are commonly used to reduce stomach acid and provide relief.
PPIs are highly effective, and for many people, they’re a game-changer. But what happens when you’ve been on them for a long time? Are there risks? Should you be worried?
Let’s take a closer look.
First, What Are PPIs and How Do They Work?
Proton pump inhibitors work by blocking the enzyme in your stomach that produces acid. This helps prevent acid reflux and allows your esophagus to heal if it’s been damaged by stomach acid.
They’re often used to treat:
- GERD (acid reflux)
- Peptic ulcers
- Erosive esophagitis
- Zollinger-Ellison syndrome
For short-term use (usually 4–8 weeks), they’re considered safe and effective. But problems may arise with long-term use, which is sometimes necessary for people with chronic GERD.
What Are the Long-Term Side Effects?
While many people use PPIs without noticeable issues, long-term use—generally considered longer than 3 months to a year—has been associated with some potential side effects and risks. Here’s what you need to know:
- Nutrient Deficiencies
PPIs reduce stomach acid, which is essential for absorbing certain nutrients.
- Vitamin B12 deficiency: May lead to fatigue, memory problems, or nerve issues.
- Magnesium deficiency: Can cause muscle cramps, irregular heartbeat, or seizures in rare cases.
- Calcium malabsorption: Could contribute to weakened bones over time.
- Increased Risk of Bone Fractures
Long-term PPI use may be linked to a higher risk of hip, wrist, or spine fractures, especially in older adults. This may be due to reduced calcium absorption.
- Kidney Problems
Some studies suggest an association between long-term PPI use and chronic kidney disease or even kidney failure, especially if taken without medical supervision.
- Infections
Because stomach acid helps kill harmful bacteria:
- There’s a higher risk of Clostridium difficile (C. diff) infection, a serious gut infection that causes diarrhea.
- Some evidence links PPIs with increased risk of pneumonia, especially in hospital settings.
- Possible Link to Dementia
There have been studies suggesting a possible connection between long-term PPI use and dementia, but the evidence is not yet conclusive. More research is needed.
- Rebound Acid Hypersecretion
If you stop PPIs suddenly, your stomach may produce even more acid than before, leading to a return of symptoms. This is why it’s important to taper off slowly under a doctor’s guidance if you decide to stop.

Should You Stop Taking PPIs?
Not necessarily. For many people, the benefits of PPIs outweigh the risks—especially if GERD symptoms are severe or causing damage to the esophagus.
However, it’s a good idea to:
- Talk to your doctor regularly about whether continued PPI use is necessary.
- Use the lowest effective dose for the shortest possible time.
- Consider lifestyle changes (more on this below) that may reduce or eliminate your need for medication.
Ways to Manage GERD Without Long-Term Medication
Lifestyle changes can make a big difference in managing GERD symptoms. Here are some tips:
- Eat smaller meals and avoid overeating
- Avoid trigger foods (spicy, acidic, fried, or fatty foods)
- Don’t lie down after eating—wait at least 2–3 hours
- Raise the head of your bed to reduce nighttime reflux
- Maintain a healthy weight
- Quit smoking
- Limit alcohol and caffeine

Final Thoughts
Proton pump inhibitors are a powerful tool in the fight against GERD and acid reflux. But like any medication, they’re not without risks—especially when used long term.
If you’ve been taking a PPI for months or even years, it doesn’t mean you’re in danger, but it’s worth having a conversation with Dr Sherif – Consultant Laparoscopic and Upper Gastrointestinal Surgeon who has a specialist interest in GERD and treatments for reflux. Together, you can weigh the risks, explore alternatives, and come up with a plan that protects both your comfort and your long-term health.
Disclaimer: This blog is for informational purposes only and does not substitute professional medical advice. Always consult your healthcare provider for guidance about your specific situation.
Contact us for more information:
Dubai General Surgeon Dr Sherif Awad Specialized Care for Lasting Relief from Acid Reflux.
About Dr Sherif Awad
Dr Sherif is a leading experienced Consultant General, Laparoscopic, Upper Gastrointestinal and Weight Loss Surgeon based at Emirates Speciality Hospital (Healthcare City).