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The Hidden Dangers of Proton Pump Inhibitors

Proton Pump Inhibitors (PPI’s), which include popular brand names Omeprazole and Nexium, are among the 10 most widely used medications in the world.(1) They are prescribed to treat a range of acid-related conditions including stomach ulcers and Gastro-oesophageal-reflux-disease (GORD). PPI’s work by interfering with a system known as the “proton pump” in the cells of the stomach lining; actively reducing acid production. (2) The drugs are very effective and for many can bring relief from the chronic upset of GORD and other acid-related conditions.

So what’s the issue?

As with many medications, PPI’s are intended for short-term use only. Or to quote the NHS guidance: “PPIs should be initiated ONLY where clearly indicated and for the shortest duration that is appropriate, in order to minimise adverse effects.” (3)

Despite this, many patients end up taking PPI’s for years or even decades. This is partly because PPI’s do not cure the conditions they are prescribed to treat (and so the problem returns as soon as use is discontinued) and partly because they can cause a condition called ‘rebound acid hypersecretion syndrome’ – whereby the stomach cells overcompensate for low acid levels and go into overdrive. In both cases, coming off PPI’s often means returning to the chronic pain and misery of acid reflux disease.

So why not stay on PPI’s indefinitely?

As mentioned, the NHS advises that PPI’s should only be taken for the shortest possible time in order to minimise potential ‘adverse effects’. These include:

  • Clostridium difficile infection
  • Increased risk of bone fractures
  • Increased mortality in older patients
  • Chronic Kidney disease
  • Hypomagnesaemia
  • Vitamin B12 deficiency
  • Community acquired pneumonia

And while the risk of developing these side-effects is relatively small in the short-term, the risk increases exponentially with long-term use.

How PPI’s make reflux WORSE

In addition to the adverse effects listed above, PPI’s can wreak havoc on your body’s natural digestive processes. After all, the acid is there for a reason. Not only does hydrochloric acid help the body to break down, digest and absorb vital nutrients – it also plays an important role in the body’s defence system by eliminating bacteria and viruses to protect against infection.

Taken to the extreme, inhibition of the acid-secreting cells can lead to a condition called Hypochlorhydria (chronic deficiency of Hydrochloric acid in the stomach) which left untreated can cause damage to the gastrointestinal system, infections, and a number of chronic health issues. (4)

Low acid levels can also delay the passage of solid food through the stomach – a process known as ‘gastric emptying’. This is particularly troublesome from a reflux perspective as the longer food sits around in the stomach, the greater the pressure on the lower oesophageal sphincter (the valve that stops stomach contents re-entering the oesophagus) and the greater the chance of reflux occurring. (5) 

PPI cessation can lead to rebound reflux

Given the safety concerns and their adverse effects on digestion, reducing or stopping PPI use might sound like a good idea. But as mentioned, suddenly removing the drugs can lead to ‘rebound acid hypersecretion syndrome’ whereby the stomach cells produce an overabundance of acid. This can result in a rapid recurrence of reflux symptoms.

So what’s the answer?

The key to safely coming off PPI’s is to do so very gradually. This can be achieved by slowly reducing the dosage of the medication, or missing doses on alternate days. Another option is to replace PPI’s with a less powerful acid-blocking medication such as a H2 blocker (e.g. Zantac) which generally have less safety concerns with long-term use.

Important note: It is crucial to speak to your doctor before reducing or stopping any medication including PPI’s. For some conditions, the benefits of taking PPI’s may outweigh any potential side-effects. 

Natural Alternatives to PPI’s

What is most frustrating about the widespread use of PPI’s, is that in many cases they are prescribed unnecessarily, and that similar results can be achieved with simple diet and lifestyle changes. Switching to a whole-food diet, eliminating highly processed foods and taking care of your microbiome are generally much safer and more effective ways of beating acid reflux.

For a more in-depth look into the causes of Acid Reflux and how to cure the problem naturally, read our earlier blog post here: The Real Cause of Acid Reflux (and how to cure it permanently).

Whether you are able to eliminate PPI’s or not, one of the most effective ways to improve digestion and reduce reflux symptoms is to promote healthy stomach acid levels. As we have established, stomach acid is vital for the complete digestion and absorption of protein and other key nutrients and yet factors such as chronic stress, age, and a reliance on PPI’s, can dramatically reduce our production. 

Betaine HCL

A simple but highly effective way to increase acid levels is to take Betaine HCL (a supplemental form of stomach acid) before each meal. This may seem counter-intuitive given that acid causes the pain we associate with reflux, but this is only the case if acid makes contact with the delicate lining of the oesophagus. Our stomachs themselves are designed to withstand a highly acidic environment, with an optimal pH level being around 1.5, and it is usually only in the case of ulcers (most often caused by a bacterial infection of H-pylori) that acid can cause issues in the stomach. (6)

Warning: Betaine HCL should not be taken if you have an active stomach ulcer, active gastritis or esophagitis. If in any doubt, seek medical advice. Betaine HCL should not be taken on an empty stomach unless it is followed immediately by a substantial meal.

Apple Cider Vinegar

Apple cider vinegar is another great way to promote healthy stomach acid levels and boost digestion. Although ACV has been linked to a wide range of health benefits (many of which have little evidence to back them up) we do know that it’s naturally acidic and antimicrobial – both really helpful properties if you are suffering from low stomach acid. Much like Betaine HCL, ACV is best taken shortly before a main meal to re-establish an optimum gastric pH and stimulate the release of key digestive enzymes.


PPI’s are one of the most widely prescribed medications in the world. They are very effective in treating acid-related conditions such as Gastro-oesophageal-reflux-disease (GORD) but are intended for short term use only. This is because they are associated with a number of adverse health effects when taken long term. In addition to this, PPI’s can wreak havoc on the body’s natural digestive processes, raising the internal pH of the stomach and slowing gastric emptying. Although it may not be possible for some individuals to eliminate PPI use completely, addressing low stomach acid levels by taking a supplemental form of acid prior to each meal, can have a positive impact on digestion and potentially reduce the incidence of reflux.








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