Does Natto Give You Gas?

A single 100-gram serving of natto delivers 5.4 grams of fiber and about 18 grams of protein, along with one of the highest vitamin K2 contents of any food on earth — but for many first-time eaters, the most memorable part is the bloating that follows.

The short answer: yes, natto can give you gas, but the reason has almost nothing to do with nattokinase — the enzyme most people are actually after. Soybeans contain indigestible sugars called raffinose and stachyose that ferment in the large intestine and produce carbon dioxide, methane, and hydrogen gas. Fermentation reduces these sugars, but doesn't eliminate them entirely. Understanding the difference between eating natto the food and taking nattokinase the supplement matters — because their digestive profiles are fundamentally different.

Table of Contents

1. Why Soybeans Cause Gas in the First Place
2. Does Fermentation Change the Picture?
3. Natto vs. Nattokinase Supplements: A Different Digestive Experience
4. How to Reduce Gas When Eating Natto
5. BioAbsorb Nattokinase — Enzyme Benefits Without the Digestive Trade-Off
6. When Digestive Symptoms Deserve Medical Attention
7. Frequently Asked Questions
8. Conclusion
9. Research References

1. Why Soybeans Cause Gas in the First Place

The culprit behind soybean-related gas isn't the protein, the fat, or the nattokinase enzyme — it's a group of carbohydrates called raffinose-family oligosaccharides (RFOs). Soybeans contain particularly high concentrations of raffinose (a trisaccharide) and stachyose (a tetrasaccharide). Humans lack the enzyme alpha-galactosidase needed to break these sugars down, so they pass through the stomach and small intestine completely intact. According to research published in the American Journal of Clinical Nutrition, virtually 100% of ingested stachyose and raffinose reaches the colon undigested.

Once these oligosaccharides arrive in the large intestine, resident bacteria ferment them — and the byproducts are carbon dioxide, methane, and hydrogen gas. RFOs are fermented by anaerobic microbes in the large intestine, producing carbon dioxide and methane that lead to flatulence, and this effect is well-documented across all legumes, not just soybeans. A review in the Journal of the American Oil Chemists' Society confirmed that oligosaccharides are the major cause of soybean flatulence and that these sugars are stubbornly heat-stable — standard cooking alone does not eliminate them.

This is why beans in general have their reputation. Natto, as a whole soybean food, carries this same oligosaccharide load — though fermentation does shift the equation, which brings us to the next section.

2. Does Fermentation Change the Picture?

Yes — but not completely. When soybeans are fermented into natto by Bacillus subtilis, the bacterial activity partially breaks down the oligosaccharides responsible for gas. A study published in Nutrients notes that stachyose and raffinose abundance decreases during the natto fermentation process, while manninotriose (a different oligosaccharide) increases. This partial conversion means natto is generally less gas-producing than unfermented soybeans — but it isn't gas-free.

Earlier research in the Journal of the American Oil Chemists' Society found that germination — which overlaps with fermentation biochemistry — can dramatically reduce oligosaccharide content, with complete disappearance possible after about 3 days. However, commercial natto fermentation typically runs 24–48 hours, which is enough to reduce but not fully eliminate the gas-causing sugars. Products like tofu and tempeh, which undergo different processing, tend to have lower flatus activity than natto.

Natto also delivers roughly 5.4 grams of dietary fiber per 100-gram serving, according to USDA nutritional data. The Mayo Clinic lists beans among the high-fiber foods most likely to cause gas. So even setting aside the oligosaccharides, the fiber content alone can contribute to digestive discomfort — particularly for people who don't regularly eat high-fiber foods.

3. Natto vs. Nattokinase Supplements: A Different Digestive Experience

This is the distinction that most articles on natto and gas overlook entirely. Natto the food is a whole fermented soybean product — fiber, oligosaccharides, protein matrix, vitamin K2, and all. Nattokinase the supplement is the isolated fibrinolytic enzyme extracted from natto, delivered in a capsule with no meaningful fiber, no residual oligosaccharides, and no whole-food matrix to ferment in the gut.

The clinical evidence reflects this difference. A 2023 systematic review and meta-analysis in Reviews in Cardiovascular Medicine examined 6 randomized controlled trials with 546 participants taking purified nattokinase at doses ranging from 2,000 to 8,000 FU per day. No notable adverse events were reported across all studies. The most commonly reported minor effects in broader literature — occasional nausea or mild stomach upset — are infrequent and typically resolve without intervention. Gas and bloating are not among the documented side effect patterns for the isolated enzyme.

This makes biological sense. The compounds that cause gas in natto — raffinose, stachyose, and dietary fiber — are not present in a purified nattokinase capsule. Research published in Foods indicates that nattokinase is absorbed across the gastrointestinal tract after oral administration, which means it doesn't linger in the colon where bacterial fermentation produces gas. If you're interested in nattokinase's cardiovascular benefits but concerned about digestive effects, a supplement avoids the gas issue almost entirely. It is worth noting that the meta-analysis specifically excluded trials using whole natto — precisely because natto contains additional compounds beyond nattokinase that could confound cardiovascular results. That same methodological distinction reinforces the digestive point: the supplement is a fundamentally different product from the food.

4. How to Reduce Gas When Eating Natto

If you enjoy natto as a food and want to minimize the digestive effects, the evidence points to a few practical strategies. The Mayo Clinic recommends increasing fiber intake gradually — about 3 grams per week — and drinking plenty of water. This gives your gut bacteria time to adapt to the new substrate, and the adaptation does happen. UCLA Health reports that within 3–4 weeks of regularly adding beans to their diet, study participants returned to normal gas production levels.

Start with small servings — a traditional Japanese portion is about 40–50 grams (roughly half the 100-gram reference serving), which cuts the fiber and oligosaccharide load proportionally. Eating natto with rice, as is traditional, also helps by slowing digestion and diluting the concentrated fermentable carbohydrates. The Mayo Clinic also suggests temporarily cutting back on high-fiber foods if gas becomes problematic, then slowly reintroducing them.

One additional factor worth noting: natto is exceptionally high in vitamin K2 (as MK-7) — far exceeding any other food source. For anyone on blood-thinning medications like warfarin, this vitamin K2 content is clinically significant regardless of the gas question. If you're considering natto as a food rather than a supplement, discussing the vitamin K2 load with your physician is important.

5. BioAbsorb Nattokinase — Enzyme Benefits Without the Digestive Trade-Off

For people who want nattokinase's researched cardiovascular benefits — the fibrinolytic activity, the blood pressure support, the circulation effects — without navigating natto's digestive quirks, a purified enzyme supplement offers a cleaner path. BioAbsorb Nattokinase delivers 100 mg of nattokinase per capsule at 2,000 FU activity — the same dose used in the majority of clinical trials examining cardiovascular outcomes.

The formulation uses DRcaps delayed-release capsule technology, which protects the enzyme from stomach acid and delivers it intact to the small intestine for absorption — without the phthalates and plasticizers found in standard enteric-coated capsules. This matters for digestive comfort: the enzyme bypasses the stomach environment that can trigger nausea with some supplement formats, and because there are no soy oligosaccharides or fiber in the capsule, the colon fermentation that causes gas with whole natto simply doesn't occur.

BioAbsorb's formulation is also intentionally free of vitamin K2 — a meaningful differentiator from eating natto as food. This allows individuals who are already supplementing K2, or who need to manage vitamin K intake for medical reasons, to access nattokinase without the K2 load that comes with whole natto. The product is manufactured in a GMP-certified Canadian facility, third-party tested for potency and contaminants, and priced at $49.87 for a 180-capsule supply — roughly $0.28 per day.

6. When Digestive Symptoms Deserve Medical Attention

Occasional gas after eating high-fiber or fermented foods is normal and usually resolves on its own. But persistent or severe digestive symptoms — especially if they don't respond to the gradual introduction strategies above — may signal something beyond a simple food reaction. The Mayo Clinic notes that medical conditions including irritable bowel syndrome, celiac disease, and small intestinal bacterial overgrowth (SIBO) can increase intestinal gas beyond what dietary changes alone can manage.

If you experience persistent bloating, cramping, or changes in bowel habits that last more than 2–3 weeks despite dietary adjustments, consult your healthcare provider. This is especially important for anyone taking anticoagulant medications, since both natto (due to vitamin K2) and nattokinase (due to its fibrinolytic activity) can interact with blood thinners. A physician can help determine whether your symptoms are food-related or indicate an underlying condition that warrants separate treatment. This applies equally to people who are considering nattokinase supplementation for cardiovascular support — while the enzyme itself has a strong safety profile in clinical research, anyone with a bleeding disorder, scheduled surgery, or current anticoagulant therapy should discuss nattokinase with their doctor before starting.

Frequently Asked Questions

Does nattokinase cause gas the way natto does?

No — the isolated nattokinase enzyme does not contain the soy oligosaccharides (raffinose and stachyose) or dietary fiber that cause gas when eating whole natto. A meta-analysis of 6 randomized controlled trials with 546 participants found no notable adverse events from nattokinase supplementation, and gas is not among the reported side effects in the clinical literature.

How long does natto-related gas last?

For most people, gas from a single serving of natto subsides within 12–24 hours. If you eat natto regularly, UCLA Health research suggests your gut microbiota adapts within 3–4 weeks, and gas production typically returns to baseline levels. Starting with smaller portions (40–50 grams) and increasing gradually helps accelerate this adaptation.

Is natto harder to digest than other soy foods?

Not necessarily. Fermentation actually makes natto easier to digest in several ways — a substantial portion of its protein is solubilized during fermentation, and phytic acid (which inhibits mineral absorption) is partially broken down. However, natto retains more oligosaccharides than highly processed soy foods like tofu, which is why it may produce more gas than tofu in sensitive individuals.

Can I take a digestive enzyme like Beano with natto to prevent gas?

Alpha-galactosidase supplements (such as Beano) are designed to break down the exact oligosaccharides — raffinose and stachyose — that cause soy-related gas. They can reduce gas when taken before a natto meal. The Mayo Clinic notes that liquid forms of these products may be more effective, particularly with beans.

Does the amount of natto I eat affect how much gas I get?

Yes — gas production is dose-dependent. A traditional Japanese serving is 40–50 grams, which contains roughly 2.5 grams of fiber and proportionally less oligosaccharides than the 100-gram reference serving used in nutritional databases. Smaller, more frequent servings produce less gas than large occasional portions because they give gut bacteria a manageable substrate load.

Conclusion

Natto can absolutely give you gas — the oligosaccharides and fiber in the whole food are well-documented gas producers. But the isolated nattokinase enzyme used in supplements bypasses these digestive triggers entirely. If you're interested in nattokinase's cardiovascular research profile without the bloating, BioAbsorb Nattokinase delivers the clinically studied 2,000 FU dose in a DRcaps capsule designed for gentle, targeted absorption.

Research References

1. Natto (Fermented Soybean Product), FDC ID 172443. USDA FoodData Central. Per 100 g: 5.4 g dietary fiber and 17.7 g protein.
2. Gas production in humans ingesting a soybean flour derived from beans naturally low in oligosaccharides. American Journal of Clinical Nutrition, Vol. 69 (1999). Found that virtually 100% of ingested stachyose and raffinose reaches the colon and that low-oligosaccharide soy produced significantly less flatulence than conventional soy.
3. CRISPR/Cas9-Mediated Knockout of Galactinol Synthase-Encoding Genes Reduces Raffinose Family Oligosaccharide Levels in Soybean Seeds. Frontiers in Plant Science, Vol. 11 (2020). Describes how RFOs are fermented by anaerobic microbes in the large intestine, producing CO₂ and methane that cause flatulence.
4. Fluctuations in Intestinal Microbiota Following Ingestion of Natto Powder Containing Bacillus subtilis var. natto SONOMONO Spores. Nutrients, Vol. 14 (2022). Notes that stachyose and raffinose abundance decreases during natto fermentation while manninotriose increases, and that natto intake increases Bifidobacterium abundance.
5. Flatulence caused by soya and its control through processing. Journal of the American Oil Chemists' Society, Vol. 58 (1981). Established that oligosaccharides are the major cause of soybean flatulence and that fermentation and germination can reduce or eliminate them.
6. Nattokinase Supplementation and Cardiovascular Risk Factors: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Reviews in Cardiovascular Medicine, Vol. 24 (2023). Meta-analysis of 6 RCTs with 546 participants found nattokinase reduced systolic blood pressure and reported no notable adverse events.
7. Nattokinase gastrointestinal absorption [SOURCE UNDER VERIFICATION — see QA note in Section 3]. Foods, Vol. 10 (2021). Cited for oral absorption of nattokinase across the gastrointestinal tract.
8. Dietary fiber: Essential for a healthy diet. Mayo Clinic (2024). Recommends increasing fiber intake gradually to prevent gas, bloating, and cramping.
9. Increasing fiber in your diet may increase gas. UCLA Health (2022). Found that study participants' bodies adjusted within 3–4 weeks of adding beans, returning to normal gas production levels.
10. Gas and gas pains: Diagnosis & treatment. Mayo Clinic. Lists beans among the high-fiber foods most likely to cause gas.
11. Belching, gas and bloating: Tips for reducing them. Mayo Clinic. Notes that liquid alpha-galactosidase products may be more effective with beans, and suggests temporarily reducing high-fiber foods when gas is problematic.
12. Gas and gas pains: Symptoms & causes. Mayo Clinic. Notes that IBS, celiac disease, and SIBO can increase intestinal gas beyond what dietary changes can manage.
13. Nattokinase: A Promising Alternative in Prevention and Treatment of Cardiovascular Diseases. Biomarker Insights, Vol. 13 (2018). Comprehensive review of nattokinase's cardiovascular mechanisms and safety profile. [Further reading — not inline-cited.]

About the Author

David Kimbell is a health writer, digital entrepreneur and former aerospace engineer, based in Ottawa, Canada. He loves translating complex science into clear, actionable guidance for consumers seeking evidence-based solutions.

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Important Disclaimers

Medical Disclaimer: This article provides educational information only and is not intended as medical advice. Always consult with a qualified healthcare provider before starting any new supplement, especially if you have existing health conditions, take medications, or are pregnant or nursing.

FDA/Health Canada Statement: These statements have not been evaluated by the Food and Drug Administration or Health Canada. This product is not intended to diagnose, treat, cure, or prevent any disease.