Soy: Health Concerns and Benefits

07/11/2023 | 5 min. read

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Opinions on soy are all over the map. There is a lot of research showing the benefits of soy consumption—and a lot of concern about its negative impact. Even as a naturopathic physician, I find the research on soy overwhelming and confusing to sift through!

So, what is correct? Is soy good for us, or should we avoid it? It all depends on the type of soy, how it is processed and prepared, who is eating it, and how much is eaten. Here is my take on soy.

Types of Soy

One reason for the conflicting opinions about soy is because it comes in so many forms.

Fresh or Dried Soybeans

Fresh young soybeans (edamame) are steamed or boiled and eaten right out of their pods or shelled and cooked in stir fries and other dishes. More mature soybeans are dried, then soaked and prepared like other beans.

Processed Unfermented Soy Products

Soy milk, tofu, soy cheese, etc., are made from pureed beans that are soaked, cooked, ground or pureed and further processed.

Soy protein isolate is protein that has been isolated from soybeans after the fat and hulls are removed. It is used in soy protein powders, flour, and concentrates.

Textured vegetable protein (TVP) is made from soy flour or concentrates, combined with other flavorings or additives and compressed into desired shapes. Examples of processed soy products made with TVP include soy hotdogs, burgers, nuggets, sausage, Tofurky, and crumbles.

Fermented Soy Foods

Many traditional soy foods in Asia, where soybeans were first domesticated, are fermented. Miso (a paste used in soups, sauces, and as a seasoning), tempeh (a meat substitute similar to a bean cake), tamari (gluten-free soy sauce), and natto (a sticky bean dish) are all made with fermented soybeans.

Benefits of Soy


Soy is an excellent form of protein. Unlike most plant foods, it is a complete protein. This means it contains all nine essential amino acids that cannot be synthesized by the body and must be consumed in the diet, so it’s particularly good for vegetarians.

Minerals, Vitamins, and Fiber

Soybeans are high in potassium, iron, magnesium, calcium, and B-vitamins. Fermentation of soy results in the production of vitamin K2, an important nutrient that helps move calcium into the bones and out of the arteries, enhancing bone health and reducing the risk of atherosclerosis. Whole soy, fermented, and some processed soy products are also good sources of fiber.

Soy Isoflavones

Soy is nature’s richest source of isoflavones. These plant compounds are classified as phytoestrogens because they have weak estrogenic effects, similar to those of endogenous estrogen (produced in our bodies). Isoflavones can bind to estrogen receptors and either exert mild estrogenic effects or prevent the binding of stronger endogenous estrogen.  

For premenopausal women who are producing higher levels of estrogen, this competitive binding can be helpful, as it blocks stronger-acting estrogen for a lower overall estrogenic effect.

Soy isoflavones can also be beneficial for menopausal women whose estrogen is naturally declining and levels are low. When phytoestrogens bind to estrogen receptors, they create a mild estrogen-like effect in an estrogen-deficient body, which can help relieve menopausal symptoms and support bone health. Some studies suggest that soy isoflavones may also help protect against breast cancer.

Soy Health Concerns

My concern comes into play when the majority of an individual’s soy intake is processed soy (soy milk, tofu, soy cheese, soy dogs, Tofurky, etc.) and when it is eaten multiple times a day. Here’s why.

A Top Allergen

Soy is one of the most common but often overlooked food allergens. I didn’t grow up eating soy and was really introduced to it when I was in naturopathic school. I couldn’t understand why I was wracked with stomach pains after eating a “healthy” meal of tofu—until I learned about its high allergic potential.

Digestion Difficulties

People who find soy hard to digest can often tolerate fermented soy products, since fermentation helps “predigest” it, which makes it easier on the gut. I can typically tolerate edamame, tempeh, miso, and tamari, but if I have soy milk, tofu, or a bar or drink containing soy protein isolate, it sounds like a convergence of whale pods are having a dynamic conversation in my belly. It is not comfortable!


Soy contains phytates and oxalates, which are classified as anti-nutrients because they inhibit the absorption of calcium, iron, zinc, and other minerals. Fermentation, used to prepare tempeh, miso, etc., neutralizes most of these anti-nutrients.


Soy is one of the most heavily genetically modified crops—94% of the soybeans planted in the U.S. are GMO. So, it is wise to always make sure the soy you are consuming is certified organic and GMO-free.

My Soy Recommendations

As you can see, soy has a number of health benefits and a number of potential concerns. I do not believe there is anything “dangerous” about soy as some claim—nor do I believe that including soy in your diet is necessary for good health.

My general recommendation is that as long as you have no problems digesting soy, you feel good after eating it, and you don’t suspect an allergy, it is fine in moderation.

Always opt for organic, non-GMO soy and do your best to choose whole, minimally processed soy foods, such as edamame rather than soy lunch meat. You’ll find miso or tempeh in our fridge much more often than you’ll find soy milk or tofu.

I also recommend fermented soy over non-fermented or processed soy products because they are better tolerated—even if your digestive system struggles with processed soy.

Dr. Briana Sinatra

Meet Dr. Briana Sinatra

Dr. Briana Sinatra is a board-certified naturopathic doctor with a vibrant practice in the Pacific Northwest. There she focuses on women’s and family health, taking a holistic approach to healthcare by empowering women with the knowledge and tools they need to live their best life now and protect their future wellness by looking at how all the systems in the body work together and how diet, lifestyle, and environment all influence health.

More About Dr. Briana Sinatra