How to protect your stomach and gut when taking naproxen

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What is Naproxen?

Naproxen is a painkiller that belongs to a group of medicines known as nonsteroidal anti-inflammatory drugs (NSAIDs). It’s widely used to relieve pain and inflammation from conditions like arthritis, injuries, period pain, and musculoskeletal disorders. Naproxen is known for being fast-acting and long-lasting.

But while NSAIDs like naproxen are effective for pain relief, they are also associated with disruption to the gut, particularly with long-term use. This includes not only irritation of the stomach lining, but also imbalances in the gut microbiome.

In this guide, we explore how naproxen affects the gut, what you can do to protect your digestive health, and how supporting your gut microbiome may reduce the long-term impact of NSAID use.

What does Naproxen do to the stomach?

Research has shown that chronic use of NSAIDs like naproxen can cause peptic ulcer disease, which is a condition that causes painful ulcers to develop in your stomach lining or small intestine.

NSAIDs like naproxen can cause stomach ulcers by inhibiting the stomach’s natural ability to protect itself from gastric acids. When the stomach is exposed to excessive acid, it can result in ulcers.

This happens because NSAIDs interfere with the stomach’s natural defence mechanisms. Specifically, they inhibit prostaglandins, compounds that normally protect the stomach lining by:

• Reducing acid production
• Promoting mucus and bicarbonate secretion
• Supporting blood flow to the gastric mucosa

Without this protection, stomach acid can damage the lining, increasing the risk of ulcers, inflammation, and gastrointestinal discomfort.

Symptoms that may indicate gut irritation from Naproxen include:

• Heartburn
• Stomach pain
• Nausea or vomiting
• Indigestion
• Diarrhoea

If you have a history of stomach ulcers or digestive issues, it’s important to speak to your doctor before using naproxen or any NSAID.

NSAIDs and the gut microbiome

While damage to the stomach lining is well known, research increasingly shows that NSAIDs also affect the gut microbiome, made up of may different types of bacteria, fungi, and other microbes that play a critical role in digestion, immunity, and inflammation.

NSAIDs like naproxen have been shown to:

• Alter the composition of gut bacteria
• Reduce microbial diversity
• Disrupt the gut barrier potentially leading to leaky gut
• Increase the risk of dysbiosis, an imbalance between beneficial and harmful bacteria

This disruption can lead to symptoms such as:

• Bloating
• Gas
• Reflux
• Irregular bowel movements
• Increased inflammation

When the gut microbiome is compromised, the risk of not only ulcers but other gastrointestinal symptoms increases. Chronic inflammation, driven by microbial imbalance, may also make pain conditions worse over time, creating a loop where more pain requires more NSAIDs.

How to protect your gut when taking NSAID's

If you’re taking naproxen, especially long term, there are steps you can take to protect both your stomach lining and gut microbiome.

Gut-friendly diet

Eating a diet rich in anti-inflammatory and fibre-rich foods good for gut health helps maintain gut barrier integrity and supports a diverse, healthy microbiome.

Include:

• Leafy greens (spinach, kale, rocket)
• Cruciferous vegetables (broccoli, cabbage, cauliflower)
• Whole grains (oats, quinoa)
• Fermented foods (kefir, sauerkraut, plain yoghurt)
• Prebiotic-rich foods (onions, garlic, leeks, asparagus)
• Polyphenol-rich foods (berries, olive oil, green tea)

Avoid excessive alcohol, ultra-processed foods, and refined sugars, which can worsen inflammation and microbiome imbalance.

Proton Pump Inhibitors

Often, a medication called a proton pump inhibitor (PPI) is prescribed alongside naproxen. Proton pump inhibitors such as omeprazole are effective at protecting the stomach when taking an NSAID like naproxen. They work to inhibit the production of stomach acid, which significantly reduces the risk of stomach ulcers and other gastric problems.

Proton pump inhibitors are commonly prescribed to treat acid reflux, stomach ulcers and gastro-oesophageal reflux disease (GORD).

NICE prescribing guidelines states that individuals using NSAID's that are at a high risk of Gastrointestinal adverse events should also be prescribed a proton pump inhibitor.

Risks of prolonged PPI use include:

• Reduced microbial diversity
• Higher risk of SIBO (Small Intestinal Bacterial Overgrowth)
• Impaired nutrient absorption (e.g. B12, magnesium)
• Increased susceptibility to gut infections (e.g. C. difficile)

Probiotics

Some research suggests that probiotic supplements may help reduce NSAID-induced gut damage by:

• Supporting mucosal integrity
• Competing with harmful bacteria
• Modulating inflammation

Strains such as Lactobacillus rhamnosus and Bifidobacterium longum may be particularly helpful. However, individual results vary — testing your microbiome can help you select targeted strains.

Take with food

Taking naproxen with or just after a meal can reduce stomach lining irritation and acid exposure. This remains good practice, especially when used occasionally.

Which NSAIDs are best for your stomach?

Taken in high doses or in the long term, most NSAIDs can cause side effects that may damage the stomach or cause ulcers. However, whereas the maximum dose of naproxen is 660mg each day, up to 1,200mg of ibuprofen can be taken each day.

It is important to talk to your doctor if you have a chronic condition that may require long-term use of an NSAID.

Prolonged NSAID's use can cause gastrointestinal complications and symptoms. It has been found that NSAID's can directly influence the composition and function of the gut microbiome, which can lead to an imbalance of the bacteria within the gut, called Dysbiosis.

Dysbiosis can present symptoms such as acid reflux, heartburn, gas, bloating, inflammation and other digestive problems. Taking a gut microbiome test can identify gut dysbiosis and help identify the root cause of your gastrointestinal symptoms. 

Some NSAIDs are also available as topical treatments, such as ibuprofen, which is contained as the active ingredient in certain gels.

Typically, Ibuprofen, paracetamol and Naproxen are the most commonly used painkillers that are used to treat a wide variety of conditions. Paracetamol, out of the three, is the safest and most widely used painkiller due to its low reported adverse effects.