Does Omega-3 Reduce Stomach Acid? Unpacking the Complex Answer

October 18, 2025 •

3 min read

While omega-3 fatty acids are widely praised for their anti-inflammatory properties, a 1999 study in the Scandinavian Journal of Gastroenterology found that fish oil can reduce gastric acid secretion, suggesting a potential role beyond general health. However, many people report a surprising side effect: acid reflux from fish oil supplements.

Quick Summary

This article explores the evidence regarding omega-3's effects on stomach acid, distinguishing a direct-action study from the common side effect of heartburn caused by supplements. It also details the broader, anti-inflammatory benefits omega-3s provide for overall gut health.

Key Points

Direct Acid Reduction: A controlled study showed that introducing fish oil directly into the small intestine can reduce stomach acid secretion.
Heartburn Side Effect: Despite direct-action research, high-dose omega-3 supplements commonly cause acid reflux or heartburn due to their fat content and capsule form.
Anti-inflammatory Action: Omega-3s are powerful anti-inflammatory agents that help reduce intestinal inflammation, which is beneficial for overall gut health.
Gut Microbiome Support: Omega-3s can increase the diversity and presence of beneficial bacteria in the gut, promoting a healthier microbial environment.
Intestinal Barrier Integrity: These fatty acids help strengthen the protective lining of the gut, which can prevent 'leaky gut' and related issues.
Symptom Management: Taking supplements with food, splitting the dose, using enteric-coated capsules, or freezing them can help minimize acid reflux side effects.
Whole Food Sources: Integrating fatty fish into your diet is an effective way to increase omega-3 intake while potentially avoiding the gastrointestinal issues associated with supplements.

The question of whether omega-3 fatty acids reduce stomach acid is not as straightforward as it seems. While controlled studies reveal a direct inhibitory effect, many individuals experience the opposite when taking common fish oil supplements. Understanding the difference between the pharmacological action and the potential side effects is key to navigating this topic for digestive health.

A Closer Look at Omega-3's Direct Impact

Research has explored the direct physiological effects of omega-3s on gastric function. A 1999 study found that administering fish oil directly into the duodenum significantly reduced gastrin-stimulated stomach acid secretion. This effect was thought to be mediated by an increase in cholecystokinin (CCK). This study indicates that, under specific conditions, omega-3s can have an acid-suppressing effect, which differs from the experience of taking oral supplements.

The Paradox: Why Supplements Can Cause Heartburn

Despite controlled study findings, many people report heartburn, acid reflux, or a fishy aftertaste from omega-3 supplements, especially at higher doses. This can happen because fish oil's high fat content can delay gastric emptying, keeping food and acid in the stomach longer. The capsule dissolving in the stomach may release the oil, leading to burping or fishy-tasting belches. The fat can also relax the lower esophageal sphincter, allowing acid into the esophagus.

Broader Digestive and Gut Health Benefits of Omega-3s

Beyond the complex direct effect on stomach acid, omega-3s offer significant indirect benefits for the gastrointestinal system by combating inflammation and supporting the gut microbiome.

Anti-inflammatory Effects

Omega-3s, particularly EPA and DHA, are powerful anti-inflammatory agents. They are precursors to specialized pro-resolving mediators (SPMs) and can reduce inflammatory markers linked to digestive disorders like inflammatory bowel disease (IBD).

Supporting the Gut Microbiome

Omega-3s can positively influence the gut microbiome by increasing the diversity of bacteria, promoting beneficial bacteria like Lactobacillus and Bifidobacterium, and supporting the production of beneficial short-chain fatty acids (SCFAs).

Improving Intestinal Barrier Integrity

Omega-3s help strengthen the intestinal lining, which acts as a barrier. By enhancing mucus production and improving the integrity of tight junctions, they can reduce intestinal permeability.

Comparison: Direct Acid Effect vs. Symptomatic Reflux


Aspect	Direct Acid Secretion (Controlled Study)	Symptomatic Reflux (Common Side Effect)
Occurrence	Observed under specific, controlled experimental conditions.	Frequently reported, especially with supplements and high doses.
Primary Cause	Intraduodenal administration of fish oil.	High fat content and the way capsules are digested.
Underlying Mechanism	Triggering the release of the hormone CCK, which suppresses acid secretion.	Delayed gastric emptying and relaxation of the lower esophageal sphincter.
Effect on Acidity	Reduces acid production in the stomach.	Can increase the presence of acid in the esophagus.

Practical Strategies for Navigating Omega-3s and Digestion

If you experience heartburn or acid reflux from omega-3 supplements, consider these strategies:

Timing and Dosage: Split doses and take with meals.
Take with Food: Always take supplements with food to minimize discomfort.
Choose the Right Type: Try krill oil, algae-based options, or enteric-coated capsules.
Freeze Your Capsules: Freezing may reduce fishy aftertaste and heartburn.
Consider Food Sources: Increase intake of fatty fish or plant-based sources like flaxseed.

Conclusion

A 1999 study showed that fish oil can reduce stomach acid secretion in a controlled setting, but many supplement users experience heartburn due to the high fat content and delivery method. Beyond this, omega-3s significantly benefit gut health through anti-inflammatory effects, supporting the gut microbiome, and strengthening the intestinal barrier. Managing potential side effects with practical strategies allows individuals to still gain the gut health benefits of omega-3s.

Frequently Asked Questions

Fish oil supplements can cause acid reflux because of their high fat content, which can delay stomach emptying. Additionally, the capsule can sometimes release the oil into the stomach, causing a fishy burp or heartburn.

To prevent heartburn, take your omega-3 supplements with a meal to help with digestion. Other strategies include splitting your dosage, choosing enteric-coated capsules, or freezing the capsules.

Yes, omega-3 fatty acids have significant benefits for overall gut health. They act as powerful anti-inflammatory agents, support a diverse and healthy gut microbiome, and help improve the integrity of the intestinal barrier.

Fish oil is a major source of the two most beneficial types of omega-3 fatty acids, EPA and DHA. While 'omega-3' refers to the class of fatty acids, 'fish oil' refers to the supplement source.

Yes, plant-based sources like flaxseed, chia seeds, and walnuts provide alpha-linolenic acid (ALA), a type of omega-3. While ALA is less efficiently converted to EPA and DHA, consuming these whole foods may be gentler on the stomach than concentrated oil supplements.

Eating fatty fish, such as salmon or sardines, is less likely to cause heartburn than supplements. The fat is contained within the fish protein, which the body processes differently than the concentrated oil in a capsule.

If you experience reflux, first try the management strategies, such as taking the supplement with food or adjusting the dose. If symptoms persist or are severe, consult your healthcare provider to discuss alternative omega-3 sources or different formulations.