The Hidden Dangers of Long-Term PPI Use - From Bone Health to Digestion

With party season in full swing, so many people are bracing themselves for the discomfort that comes with festive meals, rich foods, and late nights. And if you’re relying on PPIs to get through it, you’re definitely not alone — but understanding what long-term use does behind the scenes is more important than ever.

This blog is the first in a series of three. It explores how PPIs really work, why symptoms often return despite medication, and the deeper impact they can have on digestion and bone health over time.

So if eating out fills you with dread instead of excitement, this is essential reading. You deserve to enjoy this time of year without fear of pain or discomfort.

What are Proton Pump Inhibitors (PPIs)?

Proton Pump Inhibitors (PPIs) such as omeprazole, lansoprazole, esomeprazole and pantoprazole have become some of the most commonly used medications worldwide. They can be incredibly helpful for short-term relief of heartburn, gastritis or ulcer-related discomfort. But when used for months or even years—often without regular review—their impact extends far beyond calming acid symptoms.

What many people don’t realise is that stomach acid isn’t the enemy. It plays a crucial role in breaking down food, supporting nutrient absorption, maintaining a healthy microbiome and defending the body against harmful pathogens. When acid levels are suppressed for too long, other systems have to compensate, and over time that can create unexpected consequences.

This is where the long-term risks of PPIs begin to surface—not just for bone health but for digestion and overall metabolic wellbeing.

The Overlooked Role of Stomach Acid

Hydrochloric acid (HCl) in the stomach helps digest proteins, stimulates digestive enzymes, assists with mineral absorption and signals the rest of the gut to prepare for incoming food. It’s also one of your first lines of defence against harmful microbes.

PPIs switch off or greatly reduce this acid production. While this brings quick symptom relief, the digestive system depends on adequate acidity to function smoothly. Low acid means the stomach can’t do its job properly and that has a ripple effect on the entire digestive tract.

How PPIs Disrupt Healthy Digestion

When acid levels remain low:

1. Protein digestion becomes impaired

Stomach acid is essential for breaking down protein into smaller, usable components. Without enough acid, proteins remain only partially digested. This can lead to:

• bloating and heaviness after eating

• undigested food fermenting in the stomach (with lots of gas)

• reduced availability of amino acids needed for muscle repair, hormones, enzymes and neurotransmitters

Over time, poor protein breakdown may even affect energy levels, skin health and immune resilience.

2. Digestive enzyme activity decreases

Pepsin, the main stomach enzyme for protein digestion, requires an acidic environment to work. When the environment becomes too alkaline due to medication, pepsin becomes less active, slowing digestion even further.

This can create a cycle where food sits longer in the stomach, increasing the feeling of reflux—not reducing it.

3. Mineral and vitamin absorption drops

Low stomach acid significantly affects the body’s ability to absorb key nutrients, especially:

• Calcium

• Magnesium

• Iron

• Zinc

• Vitamin B12

These nutrients are vital for energy, bone strength, neurological function, mood balance and immune health. Poor absorption over time can quietly contribute to chronic deficiencies.

4. Bacterial overgrowth becomes more likely

Stomach acid helps control microbial balance by neutralising harmful bacteria. With long-term suppression, the upper digestive tract becomes more vulnerable to:

• higher counts of unwanted bacteria

• small intestinal bacterial overgrowth (SIBO)

• increased gas, bloating, and irregularity

  
  

Many people are surprised to discover that the bloating they are treating with PPIs is often caused or worsened by long-term acid suppression.

5. Food sensitivities may develop more easily

When food isn’t fully broken down, larger protein fragments can enter the small intestine, where the immune system may start reacting to them. This can increase sensitivity to foods that were previously well-tolerated.

The Long-Term Consequences Nobody Talks About

While PPIs may be essential in certain medical scenarios, many people remain on them far longer than intended. The research increasingly points to several potential long-term complications:

1. Bone Density Loss

Reduced stomach acid can impair calcium absorption, contributing to reduced bone mineral density over time. This increases the risk of:

• osteoporosis

• hip fractures

• vertebral fractures

  
  

Older adults, post-menopausal women and individuals with low body weight are particularly at risk.

2. Chronic nutrient deficiencies

Magnesium, B12, iron, and zinc depletion can manifest slowly, often mistaken for ageing or stress. Symptoms may include:

• fatigue

• restless legs

• hair loss

• numbness or tingling

• muscle cramps

• low mood

  
  

3. Increased risk of infections

With weakened acid barriers, the body becomes more vulnerable to gastrointestinal infections. Older adults and those with chronic conditions may be especially susceptible.

4. Cardiovascular and kidney concerns

Some research has linked long-term PPI use to:

• chronic kidney disease

• acute interstitial nephritis

• potential cardiovascular risks, including altered nitric oxide metabolism

  
  

While more research is needed, the associations highlight the importance of medical supervision when using PPIs beyond short-term relief.

5. A gut–brain health impact

Chronic B12 and magnesium deficiency can influence mood, cognition, and sleep quality, while disrupted microbiome balance can affect inflammation and immunity.

What You Can Do to Protect Your Health?

The goal isn’t to abruptly stop your medication or to create fear—it’s to empower you with knowledge so you can make informed choices.

• Review your need for long-term PPIs

  Discuss with your healthcare provider whether ongoing use is necessary or whether a step-down approach is appropriate.

  
  

• Support digestion naturally

  A few gentle steps can gradually rebuild healthy digestion:

  • eat slowly and chew thoroughly

  • avoid overeating

  • include bitter foods like rocket, watercress, and dandelion greens

  • maintain good hydration

  • reduce processed foods that stress digestion

    
    

• Strengthen bone health.

  Incorporate:

  • calcium-rich foods

  • vitamin D

  • weight-bearing activity

  • adequate protein

  • outdoor movement and sunlight

    
    

• Consider additional testing

If you’ve been on PPIs long term, it may be worth discussing:

• bone density scans

• B12, iron, magnesium and zinc testing

• stool or breath tests if digestive symptoms remain unresolved

• Don’t stop medication suddenly!!

  Rebound acid production can be significant. A structured, supervised approach is safer and more comfortable.

The Bottom Line

PPIs have an important place in medical care, but they’re not free from consequences when used long term. Understanding how they influence digestion, nutrient status and bone health gives you the clarity you need to protect your wellbeing now and for years to come.

In next week's post I will I break down what drives GORD which stands for Gastro-Oesophageal Reflux Disease, the habits that make symptoms worse (especially during party season), and the natural changes that can help you move through celebrations with more comfort and confidence.

If you want to enjoy this season without the fear of flare-ups, this one is for you 💛.

How Can I Support You?

If you're ready to work on the root causes of reflux rather than endlessly managing symptoms, there are several ways we can move forward together.

In an ideal world, everyone struggling with reflux or digestive discomfort would follow a Metabolic Balance® personalised nutrition plan. It’s one of the most effective ways to rebalance digestion, stabilise metabolism, and reduce reflux naturally, because it’s entirely tailored to your unique biochemistry. (I got rid of reflux in a matter of days!)

But I also understand that committing to a full metabolic transformational programme isn’t always possible—especially with the current economic challenges many people are facing.

That’s why I also offer 3- and 6-month “Reflux Recovery” packages, designed specifically for those who want structured support without the deeper commitment of a full personalised nutrition plan. These programmes combine targeted nutritional and lifestyle recommendation with guidance grounded in pharmacist-backed training in reflux management and safe PPI weaning.

✨ You don’t have to navigate this alone, and you certainly don’t have to stay stuck with uncomfortable symptoms. If you’d like to learn more or explore which option might suit you best, you can find all the details on my website.

Alternatively, click here to complete an enquiry form or book a free call. Let’s explore how we can work together to get you feeling your best and get rid of this pesky reflux for good.

With warm and nourishing wishes,