Long-term PPI use is common, but not always well understood. Proton pump inhibitors (PPIs) help millions manage acid reflux, GERD, ulcers, and esophageal inflammation—but staying on them long-term may carry risks like nutrient deficiencies, infections, and fractures.
Part 1: Understanding PPIs — Benefits, Risks and Overuse
If you’ve ever dealt with heartburn, ulcers, or reflux, chances are you’ve heard of proton pump inhibitors—or maybe you’re taking one right now. These medications—like omeprazole or pantoprazole—are commonly prescribed to reduce stomach acid and allow healing.
And when used appropriately, they can be incredibly effective. PPIs have helped countless people recover from erosive esophagitis, manage GERD, treat ulcers, and prevent dangerous complications from untreated reflux such as esophageal cancer.
But while these medications offer powerful benefits, they’re also often misunderstood and overused. They are powerful medications and honestly, work wonders because the alternatives are often far riskier than these meds themselves. However, I will be the first to admit that many of my patients are on them for a little longer than I would like—for months or even years—without reevaluation, a taper plan, or support for lifestyle changes that could help them move forward.
Let’s take a closer look at the true benefits and risks, and what to consider if you’re currently on a PPI.
"Chronic PPI use has been associated with nutrient malabsorption, including vitamin B12 deficiency, particularly among older adults."
What PPIs Do and Why They’re Prescribed
PPIs block acid production at the source—by shutting off the proton pumps in the stomach lining. This makes them highly effective for conditions such as:
Heartburn, GERD (acid reflux)
Stomach or duodenal ulcers
Healing erosive esophagitis
Part of the treatment for Helicobacter pylori infections (a bacterial infection of the stomach that can increase risk of ulcers and even cause a type of stomach cancer)
Barrett’s esophagus (pre-cancerous changes of the esophagus)
And quite honestly, if you’ve landed in a Gastroenterology clinic, there’s a good chance you’re already on long-term PPI use—even if no one’s clearly explained why.
What Happens When You Stay on Them Too Long?
Problems arise when long-term PPI use continues without a clear medical reason or follow-up plan. acid for months or years can lead to some of the following:
Vitamin B12, magnesium, iron, and calcium absorption may be impaired over time (Lam et al., 2013; Faulhaber et al., 2013).
Clostridioides difficile infections and small intestinal bacterial overgrowth (SIBO) due to reduced gastric acid defense (Deshpande et al., 2012; Freedberg et al., 2017).
Increased risk of hip, wrist, and spine fractures, particularly in older adults and postmenopausal women, due to impaired calcium absorption (Yu et al., 2011; Targownik et al., 2006).
Higher risk of community-acquired pneumonia and aspiration pneumonia, especially in hospitalized or older patients (Eom et al., 2011).
There’s also been some associations related to dementia, but so far the evidence is inconclusive and no causation has been found. This is likely confounded by other health conditions as elderly patients often have many other medical issues that happen to require them to take a PPI to protect their stomach and digestive tract from complications of their other medications such as aspirin or ibuprofen use.
Some of the same patterns behind long-term PPI use—like chronic inflammation and metabolic dysfunction—can also contribute to fatty liver. Learn more about fatty liver disease symptoms and treatment.
What Are the Alternatives?
✅ Lifestyle Adjustments
Eat smaller meals
Avoid food 2–3 hours before bed
Limit caffeine, alcohol, spicy/fatty foods
Elevate the head of your bed
Address stress with breathwork or movement
✅ Milder Medication Options
H2 blockers like famotidine (Pepcid), cimetidine (Tagamet)
Antacids and alginates for short-term relief like Tums, Rolaids, milk of magnesia, Alka-Seltzer, and Gaviscon
These approaches can reduce reliance on daily acid suppression.
Part 2: Staying on PPIs Too Long? When to Reevaluate, Taper Safely, and Support Healing Naturally
In Part 1, we talked about how proton pump inhibitors (PPIs) work, their lifesaving benefits for people with ulcers, reflux, and esophageal inflammation, and the potential risks of long-term PPI use.
And while it may surprise some, PPIs are actually considered safer than many over-the-counter medications people take daily, like Tylenol (acetaminophen), when used correctly.
So what is the issue?
Too often, people start PPIs without a clear plan for follow-up. They stay on them for months or even years without reevaluation. They’re not told how to taper off, or how lifestyle changes might support healing in the first place. Over time, this can lead to some of the possible side effects we talked about previously—not because PPIs are dangerous, but because they weren’t used with intention.
Let’s talk about how to know when it’s time to pause, reassess, and move forward with a plan.
"The absolute risks of long-term PPI use are relatively low but become clinically meaningful in certain populations over time."
When Staying on a PPI Is the Best Choice
Not everyone needs to stop a PPI. For people with:
Barrett’s esophagus
Esophagitis (inflammation of the esophagus) which can range from mild to severe erosive esophagitis
A history of bleeding ulcers (peptic ulcer disease)
A hiatal hernia
Persistent reflux symptoms
Older than age 65 and on long-term aspirin
…long-term use may be medically necessary. In these cases, the benefits almost always outweigh the risks.
If that’s you, this article isn’t about pushing you off your medication. It’s about helping you understand the why—and ensuring you’re getting holistic support along the way.
But What If You Were Put on a PPI Just in Case?
This is where things get muddy. Many people are prescribed PPIs for various reasons such as during a hospital stay, after vague symptoms that are thought to possibly be reflux, or while taking certain painkillers. But the problem is, they’re never taken off—resulting in unnecessary long-term PPI use without a clear reason.
If your original symptoms have resolved, this is a good time to revisit the conversation with your provider and ask:
Why am I still on this?
What would a safe taper look like for me?
Are there things I can do with diet and lifestyle to support my healing?
How to Safely Taper Off a PPI
If your physician agrees it’s time to try tapering, don’t stop cold turkey if you have been taking PPIs for more than a few months.
It can often cause rebound acid production and cause you to actually have worse heartburn or reflux symptoms, leaving you even more uncomfortable than you started. Usually, we like to taper the dose slowly over time to give your body time to adjust. So make sure to discuss with your physician to come up with a good plan.
A smart tapering plan might include:
Reducing your dose gradually (e.g., every other day, then every 3 days)
Adding an H2 blocker (like famotidine) during the transition
Keeping a symptom log to track your progress and triggers
Tapering isn’t about going off perfectly. It’s about giving your body a chance to adjust slowly.
Rebuilding and Supporting Your Gut After PPI Use
Once you’re tapering or off a PPI, the next step is rebuilding strong, resilient digestion. It takes about 4 weeks to rebuild the microbiome.
You may want to explore:Increase fiber intake—dietary fiber has been shown to reduce reflux symptoms and improve esophageal motility (Morozov et al., 2018).Consider eating a Mediterranean-style diet—it was found to significantly reduce the frequency and severity of reflux symptoms in a randomized controlled trial. This diet emphasizes olive oil, vegetables, legumes, whole grains, fruits, and limited red meat (Romeo et al., 2023).
Probiotic support such as Saccharomyces boulardii (i.e. Florastor) (to rebalance after acid suppression, under guidance)
Fermented food products such as yogurt, kimchi, sauerkraut, and kombucha
- Consider eating a Mediterranean-style diet with alkaline water — in one study, 62.6% of patients on this diet had clinically meaningful symptom improvement versus 54.1% on PPIs (≥ 6-point reduction in Reflux Symptom Index) (Zalvan et al., 2017).
The Bottom Line
PPIs can be a critical part of healing—and for some, they remain the best option long-term. But for many, the goal is to use them when necessary and phase them out when possible.
If you’ve been on long-term PPI use (more than 8–12 weeks) and you’re unsure why, it might be time for a check-in. A safe, gradual taper combined with gut-supportive strategies could help you take the next step.
Book your FREE 20-minute GI Health Consultation today to discuss your PPI use and get personalized guidance on safely supporting your digestive health.
References
Deshpande, Abhishek, et al. Association Between Proton Pump Inhibitor Therapy and Clostridium difficile Infection: A Meta‑Analysis. Clinical Gastroenterology & Hepatology, vol. 10, no. 3, 2012, pp. 225–233.
URL: https://pubmed.ncbi.nlm.nih.gov/22019794/
Eom, Chang Soo, et al. Use of Acid-Suppressive Drugs and Risk of Pneumonia: A Systematic Review and Meta-Analysis. CMAJ, vol. 183, no. 3, 2011, pp. 310–319.
URL: https://www.cmaj.ca/content/183/3/310
Faulhaber, Gabriele A., et al. Effect of Proton Pump Inhibitors on Magnesium Metabolism: A Systematic Review. PLoS One, vol. 8, no. 11, 2013, e82985.
URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082985
Freedberg, Daniel E., et al. The Risks and Benefits of Long-term Use of Proton Pump Inhibitors: Expert Review and Best Practice Advice from the American Gastroenterological Association. JAMA Internal Medicine, vol. 177, no. 3, 2017, pp. 393–402.
URL: https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2599857
Lam, Justin R., et al. Proton Pump Inhibitor and Histamine 2 Receptor Antagonist Use and Vitamin B12 Deficiency. JAMA, vol. 310, no. 22, 2013, pp. 2435–2442.
URL: https://jamanetwork.com/journals/jama/fullarticle/1788456
Targownik, Laura E., et al. Use of Proton Pump Inhibitors and Risk of Osteoporosis-Related Fractures. JAMA, vol. 296, no. 24, 2006, pp. 2947–2953.
URL: https://jamanetwork.com/journals/jama/fullarticle/204479
Yu, Elaine W., et al. Use of Proton Pump Inhibitors and Risk of Fracture in Older Adults. BMJ, vol. 342, 2011, d593.
URL: https://www.bmj.com/content/342/bmj.d593
Zalvan, Craig H., et al. A Comparison of Alkaline Water and Mediterranean Diet vs Proton Pump Inhibition for Treatment of Laryngopharyngeal Reflux. JAMA Otolaryngology–Head & Neck Surgery, vol. 143, no. 10, Oct. 2017, pp. 1023–1029.
URL: https://pubmed.ncbi.nlm.nih.gov/28880991/