Soy was on the endo-enemy #1 list when I was first reading about the endo diet over a decade ago, right up there with red meat and dairy. So it’s interesting that, like red meat and dairy, soy is also in a gray area.

While researching my book, it became very clear that instead of soy being wholly damaging, its ability to harm or help depends on sourcing, processing, and overall soy consumption. That means soy foods can support healing in some contexts and worsen endometriosis in others.

So let’s dig into some of the myths and truths behind soy intake and endometriosis risk, and how to decide if soy is right for you.

Endometriosis Risk and Phytoestrogen Intake

The original theory on why soy was bad for endo was based on a class of phytonutrients called phytoestrogens. Phytoestrogens chemically resemble estrogen and can mimic estrogen by attaching to the estrogen receptor. Since endometriosis lesions can have up to 140 times more estrogen receptors than normal endometrial tissue, the fear was that eating soy foods might worsen endometriosis by fueling growth.

Yet, ongoing research suggests that phytoestrogens may actually have anti-estrogenic effects, leading to a lower overall concentration of active estrogen available. [1] The way this works is that phytoestrogens “steal the seat,” attaching to receptors without acting like true estrogen, leaving fewer endogenous estrogens to drive lesion growth.

This may be why studies suggest diets higher in phytoestrogens — including soy isoflavones — are associated with a lower risk of advanced endometriosis [2,3].

Soy Consumption, Phytates, and Nutrient Absorption

Just because soy has potentially helpful isoflavones doesn’t suddenly make it a perfect food. There are still some considerations. One major caution is phytates.

Soybeans harbor an incredibly high amount of phytates — more than 10x the amount found in rice [4]. Phytates act as storage protectors in seeds, but in the body they can block absorption of minerals like iron, calcium, magnesium, and zinc. This is why phytates are sometimes called “anti-nutrients.”

Research suggests that phytates in soy products can reduce mineral absorption unless properly degraded [5,6]. For example, soy milk may be marketed as a good source of calcium or iron, but without proper processing, your body may only absorb a fraction.

When phytates are broken down — through fermentation or soaking — mineral absorption improves significantly, with one study showing a significant difference in iron absorption (up to 12-fold higher when phytates were removed) [7].

Lectins, Endometriosis Symptoms, and Immune Disruption

Another consideration in soy is lectins, which are a type of phytate. Lectins can penetrate the gut barrier and provoke an inflammatory response [7]. For some people with autoimmunity or chronic conditions, lectins may worsen endometriosis related symptoms like bloating, fatigue, or digestive pain.

Lectins also make the protein in soy harder to digest. They interfere with enzymes like amylase, pepsin, and trypsin — needed for breaking down carbohydrates and proteins. This means that while soy is sometimes promoted as a complete protein with all the essential amino acids, the presence of lectins can make it a less efficient protein source.

For women already struggling with pelvic pain, chronic pelvic pain, and nutrient deficiencies, poor absorption from soy protein could contribute to ongoing symptom management challenges [8,9].

Herbicides, Soy Products, and Endometriosis Progression

Endometriosis does not like soy produced with herbicides — GM Soy allows you to spray it liberally with herbicides without it dying, why residues are always found on non-organic soy.

It’s estimated that 94% of soy grown in the United States is genetically modified (GM) to be resistant to the herbicide glyphosate. That means most soy products — like conventional soy protein powders, plant-based burgers, or unfermented tofu — carry glyphosate residues.

This matters for women with endometriosis because glyphosate is considered an endocrine disruptor. Research has linked it with hormone imbalance and may indirectly contribute to endometriosis progression.

In one study comparing GM, conventional, and organic soybeans, the GM soy had lower protein and nutrient levels, more omega-6s, and carried herbicide residues. In contrast, the organic soy had no glyphosate, higher nutrients, and a healthier fatty acid balance [12]. Choosing organic is a key factor if you’re looking to manage endometriosis effectively.

Fermented Soy and Potential Health Benefits

The best way to reduce phytates is through proper preparation, which includes soaking, sprouting, cooking, and especially fermenting. Fermentation not only degrades phytates but enhances the potential health benefits of soy.

Centuries ago, traditional cultures rarely consumed soy without fermentation. Foods like soy sauce, tempeh, miso, natto, and traditionally prepared tofu are classic examples of fermented soy products. These not only neutralize phytates but also provide probiotics, enzymes, and essential nutrients that support digestion and overall health.

Modern soy foods like processed soy milk, soy protein powders, and soy cheeses are rarely fermented, leaving phytates intact and glyphosate residues present. For women looking for symptom relief and better nutrition, fermented soy is the superior option.

Soy and Reproductive Health

Another question women often ask: does soy affect reproductive health and fertility? Here’s where things get interesting.

Some evidence suggests that phytoestrogen intake may support hormone regulation by balancing estrogen levels. By partially blocking receptors, soy can reduce estrogen dominance — one of the risk factors for endometriosis growth. This could mean potential benefits for fertility by preventing estrogen from overstimulating lesions. [13]

On the flip side, poorly prepared or overly processed soy products may interfere with the absorption of essential nutrients like zinc and iron, which are vital for menstrual cycles, fertility, and reproductive health. Deficiencies in both are also associated with endometriosis! [Read about the zinc and endometriosis and iron and endometriosis issues here]

Bottom line: the impact of soy on fertility depends on the type (fermented vs. unfermented), the amount, and your overall dietary patterns.

Soy in Plant-Based Diets and Lifestyle Strategies

Quick-made soy products often contain an abundance of phytates, blocking mineral and protein absorption.

With more women worldwide exploring plant-based diets, soy often becomes a staple. But not all soy products are created equal.

Soy milk: Opt for organic, unsweetened, and fermented versions where possible.
Soy sauce: Choose traditionally brewed, fermented soy sauce — not quick chemical versions.
Plant-based burgers and soy protein powders: These are often ultra-processed and carry herbicide residues. Homemade veggie burgers without soy or with soaked beans can be a better option.

Incorporating soy into your life should always be about lifestyle strategies that consider sourcing, processing, and balance. For example, pairing soy with healthy fats and a diverse range of whole foods can improve nutrient absorption and support overall health.

As Mumford et al. and Youseflu et al. point out in their respective studies, dietary balance — rather than exclusion or overconsumption — is one of the key factors in managing endometriosis effectively.

Endometriosis Soy Solutions: Organic and Fermented Soy for Endometriosis

Today, the art of fermenting soybeans is also nearly gone, with most of the soy we eat quickly prepared with the anti-nutrients in-tact. Not only that, but the majority is sprayed with toxic herbicides! Non-organic soy milk, soy cheeses, soy sauce (no longer fermented), soy burgers, soy protein, and quick-prepared tofu. None of these cheap soy products (on the average shelf) are fermented, all of them have herbicide residues.

With all of this in mind, we can take a step back and learn from our ancestors who enjoyed soy woven into their healthful traditions: grow it organically, ferment it or buy it traditionally prepared, and (like nearly everything) eat it in moderation.

These fundamentals, when taken together, can turn an inflammation-provoking and nutrient-robbing food into something entirely different - a food full of flavor, nutrients, and beneficial isoflavones.

Non-fermented soy products you may consider avoiding include dry soy nuts or flour, soymilk, tofu, and highly processed soy “things” (think all the soy cheeses, milk, meats, etc). Eating these foods here or there won’t “kill you,” of course, but if these make up the foundation of your diet (like me when I was a devout vegetarian) then make it a goal to kick this habit to the curb.

You can swap out soy cheese for homemade pre-soaked (to remove phytates) cashew cheese. Soy milk? Replace with your own (pre-soaked for 12 hours) nut, seed, or oat milk. Soy burgers? Make your own veggie burgers without the soy and without all the terrible vegetable oils (eww).

Traditionally fermented products that are easier to find include tempeh, miso, soy sauces, natto and fermented tofu or soy milk products. The manufacturer should market the product as fermented since this is a process that takes time and they will be proud.

It’s best to know your producer and their methods or, even better, play around with making your own at home! Check out these cool blog posts here and here if you’re interested in some fun kitchen tofu experimentation!

Final Thoughts on Soy and Endometriosis Symptoms

So, is soy consumption bad for endometriosis? The answer is: it depends on the soy products you're eating.

endometriosis diet and soy book Katie Edmonds

Unfermented, non-organic soy products (like cheap soy milk, soy cheeses, and soy protein powders) are more likely to block nutrient absorption, disrupt digestion, and carry herbicide residues. These may worsen endometriosis or contribute to poor symptom management.
Fermented soy foods (like tempeh, miso, and traditional soy sauce) provide potential health benefits, including anti-estrogenic effects that may reduce estrogen dominance and support symptom relief.
The overall impact depends on soy intake, dietary patterns, and reproductive health needs.

Soy doesn’t have to be the villain of your endo journey. With mindful choices — organic, fermented, and in moderation — you can decide if incorporating soy supports your body’s healing and your overall health.

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