Why Are Proton Pump Inhibitors Bad For You?

One of my least favourite medicines of all time are proton-pump inhibitors, aka ‘PPIs’ or ‘acid blockers’.

I’m seeing more and more people on them, who clearly shouldn’t be. It seems to me that what were once drugs that were indicated in severe gastrointestinal conditions such as stomach or duodenal ulcers are now being handed out like common over-the-counter antacids such as Mylanta or Gaviscon. Why are Proton Pump Inhibitors bad for you? Let’s have a look…

The classic picture is that of a 40-something patient who comes to see me with ongoing, severe bloating, constipation and very smelly flatulence who also has developed some food intolerances over the last few months. Looking at their medical chart I see that they have been on Nexium (a commonly prescribed PPI) for the last 18 months due to gastro oesophageal reflux (GOERD). They have a family history of GOERD and their GP put them on the meds when the patient complained of ongoing heartburn sensations.

Looking at this person’s chart I also see that they often skip breakfast, they have a mid morning snack of either toast or a muffin, followed by a sandwich for lunch and a rice, pasta or potato-based dinner. They look overweight, especially around their waist, and their tongue is coated white.

This type of high-carb, low-fibre, low-protein diet is one of the main triggers for ‘reflux’. Most people in their 30s and 40s are low in zinc and the antioxidants vitamin C, E, B6, B12, manganese, which are essential for good stomach acid production.

The low acid production is further reduced by a low protein diet (our stomach has a clever mechanism whereby it cranks up acid production if it detects protein, as protein requires acid to break down the bonds between its constituent parts called amino acids) – carbs digestion occurs partly in the mouth through the exposure to saliva (that’s why your mum was right when she kept telling you to chew your food 25 times before swallowing…), partly in the small intestine and whatever hasn’t been absorbed (fibre and resistant starch) gets fermented in the large bowel by bacteria.

Often, when people complain of reflux-type pain, they are actually experiencing low stomach acid. This leads to carbohydrate fermentation that increases pressure onto the oesophageal sphincter (the valve that separates the stomach from the oesophagus), leading to some stomach acid ‘regurgitating’ upwards into the oesophagus.


We need our stomachs to be acidic in order to digest proteins, stimulate the release of pancreatic enzymes that helps us digest fats, carbohydrates and protein and kill bad bacteria and parasites that we ingest on a daily basis.

Ongoing use of proton pump inhibitors causes severe digestive issues, including gut dysbiosis (bad bacterial balance in your colon), small intestinal bacterial overgrowth, nutrient maldigestion, gut inflammation and the potential to develop food intolerances.


By stopping the production of stomach acid, they prevent proteins from being digested efficiently. This leads to large protein complexes being found further down the digestive tract. An inflamed gut is very porous, allowing these unusual protein complexes to migrate through the gut wall where they trigger an inappropriate immune response to food antigens.