Should You Take Nattokinase On An Empty Stomach?

Updated on November 25, 2025, with new English, Latin American Spanish, and Mandarin audio versions to help readers worldwide access this content and a brand new feature, the slideshow.

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🇪🇸 Spanish (Latinoamérica)

Hoy aprenderás si la nattokinasa debe tomarse en ayunas para una mejor absorción y cómo usarla de la manera más efectiva.

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🇨🇳 中文（简体）

今天你会了解纳豆激酶是否应该空腹服用，以及这样做如何影响它的吸收与效果。

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Visual Slideshow

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Slideshow: Visual summary of how Nattokinase behaves in the stomach, how it is absorbed, and the best protocol for taking it.

About Dr. Santiano

As a physician with decades of experience in internal medicine and emergency medicine, I regularly review research on enzymes, nutrition, gastrointestinal physiology, and metabolic health. This article summarizes peer-reviewed findings on nattokinase absorption, enzyme stability, and safety. It is written to help readers understand how nattokinase behaves inside the body and how to use it responsibly.

Introduction

Can nattokinase survive the acidity of the stomach? Is absorbed by the gastrointestinal tract? Can you cook natto and retain the health benefits of nattokinase?

To answer that, we look at studies showing gastrointestinal absorption, optimum pH, and temperatures to retain nattokinase activity.

But before that, in case you are new here, I wrote about the health benefits of nattokinase and soybeans. If you already know, skip to the next section.

Why Understanding Nattokinase Absorption Matters

Nattokinase is a protein enzyme, and many people assume all orally taken proteins are fully destroyed by stomach acid. However, several studies—including in animals and humans—show that some enzymes can survive gastric conditions and retain measurable activity after intestinal absorption.

Still, laboratory and animal studies do not always translate directly into human clinical outcomes. The evidence presented here shows biochemical feasibility, but does not establish medical treatment effects. This article explains the science so readers can make informed decisions and avoid unsafe practices.

1. Natto: An application of the 80-20 Rule
2. How I Made and Appreciated Natto
3. Insulin Resistance and Atherosclerosis and the Nattokinase Solution
4. Protective Effects of Nattokinase against Strokes
5. High-Dose Nattokinase to Shrink Atherosclerosis and Lower Blood Lipids
6. Nattokinase is Nontoxic with a High Safety Margin
7. The Outstanding Vascular Effects and Dose of Nattokinase
8. Another Study shows Nattokinase can Destroy the S1 Spike Protein
9. Nattokinase Degrades the SARS-CoV-2 Spike Protein
10. Soy Foods Do Not Increase Breast Cancer Risk

Is Nattokinase Absorbed in the Stomach?

Important Safety Note

Nattokinase has anticoagulant and fibrinolytic activity. This means it can affect blood clotting.

• People on warfarin, DOACs (apixaban, rivaroxaban, etc.), aspirin, or other blood thinners should avoid nattokinase unless supervised by a physician.
• People with bleeding disorders, ulcers, or recent surgery should consult their healthcare provider before using nattokinase.

This information supports safe use and should not be interpreted as medical treatment advice.

Nattokinase is a protein. The stomach contains enzymes that digest proteins and has an acidity or pH of 1. That’s the strongest level of acidity. At that pH, some protein molecules will change shape (denature) as part of the digestive process.

Once an enzyme is denatured, it loses its biological effect. That is why some dismiss nattokinase and say that it is ineffective. They think nattokinase is useless because it will be digested in the stomach.

Maybe that wrong information drove a 47-year-old man to inject nattokinase in his arm to treat his Peyronie’s disease (bent penis).

The deformation of the penis in Peyronie’s disease is due to the contraction of connective tissue in one region of the penis. Nattokinase is believed to loosen the contracted tissue and straighten the penis so the afflicted man will live happily ever after.

Instead of taking it by mouth, the poor guy injected his arm with nattokinase, which led to the loss of blood supply in his arm and its amputation.

His story became a topic in a case report. Vascular Necrosis of the Upper Extremity After Self-Treatment for Peyronie’s Disease

Don’t be that guy!

The tragic case of self-injecting nattokinase reflects a misunderstanding of basic pharmacology. Enzymes designed for oral use should never be injected.

• Injecting nattokinase or any enzyme can destroy blood vessels, trigger massive inflammation, and lead to tissue necrosis or amputation—as shown in the published case report.

Nattokinase’s benefits occur through oral ingestion, not injection. Any off-label or experimental use should always be discussed with a qualified clinician.

pH stability of Nattokinase

A study by Lin et al. evaluated the stability of nattokinase at different pH or acid levels. pH ranges from 1, acidic, to 14, basic.

They found that nattokinase is stable at a pH range of 5 to 9. At pH 4 to 10, its activity is more than 90%.

This means that nattokinase should be taken with food. Food and water will dilute the acid in the stomach and raise the pH.

I had to research pH and absorption because some nattokinase supplements say on the bottle that they should be taken on an empty stomach. At the bottom, you will find another reason why nattokinase should be taken with food.

The graph below from Lin et al. shows the stability of the nattokinase at pH 5 to 9 and the wide range of enzyme activity from pH 4 to 10.

The pH in human tissues is around 7.35-7.45.

How to Interpret These Findings

Studies on pH stability show that nattokinase maintains activity between pH 5 and 9. This supports the idea that taking nattokinase with food—rather than on an empty stomach—reduces acid exposure and preserves enzyme activity.

It is important to note that enzyme stability in the stomach does not automatically guarantee full biological activity in human tissues. The studies referenced here include in vitro data, animal studies, and limited human observations, so conclusions must be drawn carefully.

Studies that Prove Effective Absorption and Retention of Clot-Busting Ability

Three studies show that nattokinase is well absorbed intestinally to produce health benefits.

Sumi et al. showed that nattokinase given by mouth retains its enzyme activity. They conducted an experiment where they artificially induced a blood blot in dogs. Then they gave them nattokinase capsules by mouth.

The nattokinase survived the stomach pH and got absorbed in the gastrointestinal tract. Notably, it dissolved (lysed) the experimentally induced blood clot (thrombus). That is why it is said that nattokinase has thrombolytic properties.

Fujita et al. in 1995 duplicated their findings. This time they used rats to show that nattokinase absorbed thru the intestines was able to dissolve fibrin in the blood (fibrinolytic).

The fibrinolytic, antithrombotic, lipid-lowering, and atherosclerosis-decreasing properties of nattokinase after oral ingestion of nattokinase were demonstrated by Chen et al. in their study of 1,062 human subjects.

Evidence Summary and Limitations

The studies by Sumi, Fujita, and Chen demonstrate that orally ingested nattokinase:

• can survive partial digestion,
• is absorbed through the intestines, and
• retains measurable clot-dissolving ability in animals and humans.

These results are promising.

However, we must emphasize that these experiments often involve controlled laboratory conditions or specific clinical endpoints. More large-scale, long-term human studies are needed to confirm how nattokinase behaves across different populations, health conditions, and dosing strategies.

Should Natto be Eaten Alone or With Food?

Natto, made from fermented soybeans, is a food source of nattokinase. It also contains vitamin K2 (menaquinone) and the Bacillus subtilis spore, a great probiotic.

The Bacillus subtilis is the one that ferments the soybeans to make natto.

Vitamin K2 removes the calcium from atherosclerosis and ligaments and brings them to where they should be. In the bones and teeth to make them stronger.

The spores have health benefits too. From the spores grow the Bacillus subtilis once the environment is conducive to growth. It increases the good bacteria in the gut microbiome. At the same time, it decreases the disease-causing bacteria.

I discussed those topics and more in How I Made and Appreciated Natto.

Frozen Natto: Heat it up or Not?

When natto is homemade, it is typically made in batches of about 150 or 500 gm (1.1 lbs), depending on how much you can eat. It is placed in the refrigerator after about five days to stop bacterial growth, or it will taste funny.

So it has to be put in the freezer. I put mine in plastic egg trays and take two to three at a time when I’m about to eat them.

Natto can be mixed with spaghetti, taco, and whatever you like. But I wondered, will the effects of nattokinase, vitamin K2 and the spores be preserved with freezing and cooking?

Going back to Lin et al.. Their study also looked at the temperature stability of nattokinase.

They found that the optimum temperature for nattokinase ranged from 30°C (86°F) to as high as 70°C (158°F). That suggests that natto should not be added to hot foods or else they degrade.

Instead, natto should be added and mixed with the cooked food after it has cooled down for a bit. The graph below shows that the nattokinase enzyme activity is effective until 50°C (122°F).

Meaning nattokinase is active within the normal human temperature.

Will the Vitamin K2 and Bacillus Subtilis Spores Survive the Heat?

Vitamin K2 is heat-stable. It is a fat-soluble vitamin like A, D, and E. We need fat or oil in the intestines to absorb it. That is another reason why natto should be taken with food and not on an empty stomach.

Vitamin K2 is light sensitive, so keep your natto covered while defrosting.

The spore is resistant to radiation, heat, and chemicals, based on an article in the Journal of Applied Microbiology. The Bacillus subtilis changes into its spore form when its environment is not conducive to growth and reproduction.

Practical Guidance for Readers

• Nattokinase works best when taken with food, not on an empty stomach, because food increases stomach pH and protects the enzyme from acid denaturation.
• Natto as a whole food provides not only nattokinase but also vitamin K2 and Bacillus subtilis spores, both of which have separate health benefits.
• Heating natto above ~50°C (122°F) reduces enzyme activity, so it should be added to food after cooking temperatures decline.

These are evidence-based practices derived from the available studies.

In summary, nattokinase is well absorbed in the stomach. They should be taken with food and not be exposed to high heat.

Nattokinase and the Bacillus subtilis spore probiotic are available at Amazon.

• Best Naturals Nattokinase, 2000 FU, 100 Mg, 90 Vegetarian Capsules – Third-party tested

• Bacillus Subtilis Spore Based Probiotic — High Potency Strain with Prebiotic

Or you can make your natto. How I Made and Appreciated Natto

Don’t Get Sick!

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Medical Disclaimer

This article is for educational purposes only and does not represent medical advice or treatment. Research on nattokinase is ongoing, and individual responses can vary. Do not start or stop supplements without guidance from a qualified healthcare professional, especially if you take medications that affect blood clotting.

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Related: 

1. Stay Informed: The Ultimate Guide To COVID-19 Updates
2. How to stop bleeding if on nattokinase
3. Natto: An application of the 80-20 Rule
4. Insulin Resistance and Atherosclerosis and the Nattokinase Solution
5. Protective Effects of Nattokinase against Strokes
6. How to dose Nattokinase, Bromelain, and NAC
7. High-Dose Nattokinase to Shrink Atherosclerosis and Lower Blood Lipids
8. Nattokinase is Nontoxic with a High Safety Margin
9. The Outstanding Vascular Effects and Dose of Nattokinase
10. Another Study shows Nattokinase can Destroy the S1 Spike Protein
11. Nattokinase Degrades the SARS-CoV-2 Spike Protein
12. Soy Foods Do Not Increase Breast Cancer Risk

References:

1. Lin, Hong-Ting Victor; Wu, Guan-James; Hsieh, Meng-Chien; Chang, Shun-Hsien; and Tsai, Guo-Jane (2015). “PURIFICATION AND CHARACTERIZATION OF NATTOKINASE FROM CULTURAL FILTRATE OF RED ALGA PORPHYRA
   DENTATA FERMENTED BY BACILLUS SUBTILIS N1,” Journal of Marine Science and Technology: Vol. 23: Iss. 2, Article 13. DOI: 10.6119/JMST-014-0617-1
2. Sumi, H., H. Hamada, K. Nakanishi and H. Hiratani (1990). Enhancement of
   the fibrinolytic activity in plasma by oral administration of nattokinase.
   Acta Haematologica 84, 139-143.
3. Fujita, M., K. Hong, Y. Ito, S. Misawa, N. Takeuchi, K. Kariya and S. Nishimuro (1995). Transport of nattokinase across the rat intestinal tract.
   Biological and Pharmaceutical Bulletin 18, 1194-1196.

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