|February 7, 2024

Soy – The Good, The Bad, and The Fermented

By Bulletproof Staff
Reviewed for Scientific Accuracy

Soy – The Good, The Bad, and The Fermented

For nearly 40 years, soy was one of the biggest health foods in the world. Vegetarians lauded it as a complete protein. Doctors professed its cholesterol-lowering effects. Tofu and soy milk became household staples that you still see today.

There’s a toxic side to soy, though. Not all of it is bad – in fact, certain types of soy can be quite good for you – but on the whole, soybeans come with a number of problems old-school nutritionists overlooked. Here’s a breakdown of both the good and bad sides of soy, and which types you should eat, if any.

The downsides to soy

Nutrient-sapping phytic acid

Soy is high in phytic acid, an antinutrient that keeps you from absorbing iron, zinc, calcium, manganese, and magnesium [1,2]. Phytic acid lowers the nutritional value of any meal with soy in it, and eating a lot of soy (or other foods high in phytic acid, like whole grains) puts you at risk for iron and zinc deficiencies, particularly if you’re a vegetarian getting most of your protein from tofu and other legumes.


Plants produce damaging proteins called lectins as self-defense against hungry animals. Soy is high in a specific class of lectin called agglutinin, so named because it causes your red blood cells to agglutinate (clump together) and impairs blood flow. Agglutinins can tear holes in your gut lining, allowing bacteria to leak into your bloodstream and causing autoimmune and allergic issues [3]. Agglutinins also feed E. coli in your gut, which can lead to intestinal overgrowth [4].

The lectins in soy (and in peanuts and wheat) are heat-stable [5], so cooking them won’t make a difference. Fermentation, however, does enzymatically break down soybean lectins [6]. Some people can tolerate a lot of lectins, while others are very sensitive to them. If you’re lectin sensitive, you’ll probably want to avoid most soy and soy-based products. You can learn more about lectins here.

GMO soy and glyphosate

Soy is the GMO poster child for big agriculture corporations. It was one of the earliest GMO crops to gain widespread popularity, and today more than 80% of soy grown on the planet is genetically modified. The problems with GMO crops are beyond the scope of this article; listen to this Bulletproof podcast if you want to delve deeper into them. Instead, let’s focus on pesticides.

Back in 1994, Monsanto, the world’s largest agricultural corporation, genetically modified soy to survive far greater pesticide exposure than organic soy can. Monsanto began selling their pesticide-resistant soy, which they marketed as “Roundup Ready Soy,” to complement Roundup, their pesticide. Roundup’s main ingredient, glyphosate, is carcinogenic and destroys soil integrity [7]. When studies began to find very high levels of glyphosate in Roundup Ready Soy, Monsanto responded by saying these were “extreme levels” that aren’t the norm. A subsequent study found that 70% of GMO soy has the glyphosate levels Monsanto called “extreme,” and that the nutrients in glyphosate-sprayed GMO soybeans are lower than those of organic soy [7], likely because of a drop in soil quality.

Does soy have estrogenic effects?

Soy gets a bad rap for its phytoestrogens, which bind to your estrogen receptors and mimic human estrogen. The anti-phytoestrogen sentiment comes from two things:

  • A case study of a man who developed gynecomastia (man boobs), low testosterone, and very high estrogen thanks to the soy in his diet [8].
  • Several rat studies showing that soy phytoestrogens cause infertility in male rats, and contribute to breast cancer growth in female rats [9].

Sounds scary at first. Look deeper, though, and you’ll see that the man who grew man boobs and tanked his testosterone production was drinking three quarts of soymilk a day [8], and that rats can’t metabolize phytoestrogens, but humans can [9]. Phytoestrogens do still affect your estrogen receptors [10], but the effects are milder than many people make them seem. Unless you’re subsisting entirely on tofu, soy probably won’t screw up your estrogen levels…but the mild activation won’t do you any favors, either, and it’ll unbalance your hormones more if you have low testosterone.  

Always check your labels

Soy is one of the most common food additives because it’s cheap to produce and high in MSG and protein. Nearly all processed foods contain soy in one form or another, and many non-pastured animals have soy in their feed. Always check your labels for hidden soy. The one form that isn’t a concern is soy lecithin – it’s missing nearly all the offensive components of soy.

Is fermented soy Bulletproof?

Most fresh soy and soy-based products – edamame, tofu, and textured soy/vegetable protein, for example – are bad news.  Fermented soy may be another story, depending on how well you tolerate it.

Fermentation destroys the lectins and phytic acid in fresh soy, but the fermentation process produces histamine, the same chemical your body makes during an allergic reaction. Soy sauce is quite high in histamine [11], which can cause problems in some people. To test your histamine sensitivity, try a little bit of tamari (gluten-free soy sauce) and watch for swelling, redness, post-nasal drip, congestion, or itchiness afterward. Tamari is also lower in phytoestrogens than unfermented forms of soy are…but that’s because most tamari is fermented using Aspergillus oryzae, a fungus that’s a member of the same family that contains toxic mold species. If you’re allergic to mold, you may not do well with soy sauce.

All the above points also apply to miso, the soy product used to make the miso soup that’s customary with sushi. If you can handle the histamine and aren’t allergic to Aspergillus, a little bit of tamari or miso now and then probably wouldn’t hurt. Make sure you get organic, non-GMO tamari and miso to avoid pesticides.

The best form of soy is probably natto, a polarizing fermented soybean dish that’s either delicious or the most disgusting thing you’ll ever taste, depending on who you ask. It has a potent rotting smell and a slimy consistency. It’s the most concentrated food source of vitamin K2 in the world and has a host of bacteria and fermented byproducts that can help your gut. Try natto with rice and a little hot sauce to balance out the strong taste. Like tamari and miso, natto is high in histamine [12], so be aware of how it makes you feel, and make sure you get organic natto to avoid pesticides and GMO issues.

Have you braved natto and lived to tell the tale? How do you tolerate soy? Talk about it in the comments and subscribe below for more content about improving your biology. Thanks for reading and have a great week! 


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