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Soy: Benefits and Concerns

by Thais Harris, NC
Nutrition Education Manager, Ceres Community Project
April 2016


Soybeans and soy products have fallen into the category of controversial foods, because, well, they are. I wish there was a clear cut answer to whether soy is healthy, but I haven’t found one. Here I will do my best to point out some of the health benefits of specific whole soy products (the fermented kind: tempeh, miso, tofu and natto) and some of the concerns around soy, which namely are in regards to GMO soy and highly-processed soy products (certain soy milks and tofu, soy isolates, and other derivatives).

“In ancient times in China, soy was valued as a superb green manure for the nitrogen-fixing ability of its roots. However, it was not eaten, either by animals or by people until a slow fermenting process was developed, which reduced its gas-forming indigestibility and the anti-nutrient effects of many of its constituents” (American Nutrition Association).
Soybeans are a traditional part of diets in China, Japan and Korea and are grown all around the world in Brazil, Argentina, India, Paraguay, Canada, and the United States (which produces more soybeans than any other country in the world). In countries where soybeans are consumed in whole food form rather than undergoing processing into meal and oil, these legumes often serve as an important and relatively inexpensive source of protein. However, in the US, nearly 99% of all soybeans are processed for production of animal feed and soy oil (including soy protein isolate which is a byproduct of the soy oil industry).

When it comes to any soy product, the safest option is organic, as organic foods cannot include genetically modified (GM) seeds. GM soybeans make up 94% of the soy in the United States, and the jury is still out on the safety of GM foods. The rise in food allergies and sensitivities has been linked with the introduction of GM soy in many food products. “In March of 1999, researchers at the York Laboratory in the UK were alarmed to discover that reactions to soy had skyrocketed by 50% over the previous year. Genetically modified soy had recently entered the UK from US imports and the soy used in the study was largely GM” (Institute for Responsible Technology). This is only one of many reports regarding the GM-allergy connection.

There are also issues regarding:

1. The anti-nutrients in soy such as enzyme inhibitors, which interfere with the digestion of protein. “That’s why we don’t sit down to a bowl of soybeans as we would to a bowl of pinto or black beans.” These anti-nutrients can, for the most part, be neutralized by soaking and fermenting the beans.

2. The fact that soy is the greatest food source of phytoestrogens, which are plant compounds that can mimic the physiological effects of the endogenous hormone, estrogen (Kresser). These phytoestrogens can lower testosterone levels, which is why, some might argue, tofu became a regular food for monks more than 1,000 years ago to assist with their sexual abstinence. However, some of the research shows that this estrogenic effect only takes place when eating large quantities of soy daily.

3. One last caveat is that people who do not have a reliable source of iodine should avoid soy because of thyroid complications. Isoflavones in soy can inhibit thyroid peroxidase (TPO), an enzyme involved in the synthesis of the thyroid hormones. This mostly happens when someone is deficient in iodine (Norris).

So why eat soy at all, you might ask?

There have been many reported benefits of soy, which include:

• High protein ("meat of the field”) and good protein digestibility when fermented

• Unique peptides in soybeans include defensins, glycinins, conglycinins and lunasin, providing improved blood pressure regulation, and better control of blood sugar levels

• Good source of vitamin K, especially when fermented

• Cancer-protective activity, namely lowering prostate and breast cancer risk (studies were done with small quantities of consumption)

• Some of the benefits of soy seen in Asian populations don’t necessarily translate to other cultures (ie. bone health, reduced hot flashes), which many experts believe is related to the quality of the soy products, the method of preparation (fermentation) and other nutrients consumed regularly with the soy, such as fish broth and fish sauces, seaweed, and eggs.

At Ceres we have provided only fermented versions of organic soy, such as tempeh, fermented tofu, and soy miso. We are currently only offering organic tempeh, as we have removed tofu from our menu and are using chickpea miso instead of soy miso in order to make it easier for the kitchen to accommodate our client’s food restrictions and allergies, many of which are soy related.

Most of the soybeans consumed in the US are “processed by using hexane or other solvents to remove the oil (which can be sold as cooking oil or oil to be added to other processed foods), and then we take what's left over (defatted soy flour) and either combine it with other proteins to make animal feed or wash it with water to create soy protein concentrate. Soy protein concentrate becomes the source for two forms of soy that are even more processed: TVP, or textured soy protein that can be produced through a process called extrusion, and SPI (soy protein isolate), which can be produced by making the soy protein concentrate more solubilized. SPI is used in many low-fat soy milks.” (World’s Healthiest Foods). This industrial processing creates a food product that isn’t so easy for our bodies to recognize or properly digest, and adds harmful nitrosamines (known to cause cancer) in the process (U.S. FDA). The most unfortunate use of this product is in infant formula. I personally avoid products that have SPI in them to safeguard my health – and my family’s.

Soy Milk

It is possible to make a less processed version of soy milk at home by soaking soybeans in water overnight for 12 hours; draining the soybeans and removing the outer skins; blending the soybeans with water; straining the blended mixture using a cheesecloth; then cooking and cooling the milk. Click here to check out this recipe.

When considering store-bought soy milk, it is very important to only consume it if it is organic, so that it is low on pesticide residues and isn’t genetically modified. Most soy milk brands have too much added sugar (up to 12g per 8oz) and just as with the other non-dairy milks, caution should be exercised when the milk contains additives (preservatives/thickeners). One of these additives, carrageenan, is thought to be an inflammatory agent, especially to the gut, and consistent exposure to it should be avoided (occasional exposure is considered safe).


Tofu can be made from full-fat soy milk by using salts or acids to coagulate the milk into curds that can be pressed into cakes. This is the most commonly used method. Tofu can also be made through fermentation, and used more as a condiment.


Tempeh is a traditional food made by fermenting soybeans with a starter culture and vinegar (and yes, you can make it at home). Traditional tempeh has a rich smoky flavor and aroma with a firm, nutty texture. It is a great source of vitamin B12.


Natto is another good example of a whole food form of soybean, however its taste is something to be “acquired.” Natto can be made by taking whole soybeans, adding a bacteria called Bacillus subtilis, and giving the bacteria time to ferment the beans. Natto can be quite stinky while fermenting, and you may want to isolate the natto during the fermentation time. Making natto at home is a bit more time-consuming than tempeh, and requires extra equipment


Miso paste is created from a mixture of soybeans, sea salt and rice koji that is fermented. The fermentation process creates enzyme-rich compounds, antioxidants and probiotics.

Miso is typically considered to be a high-sodium food (1 tsp contains 200-300 milligrams of sodium). However, recent research has shown that in spite of its high sodium content, miso does not appear to affect our cardiovascular system in the way that other high-sodium foods sometimes can. Since miso is not usually eaten alone, other cardio-supportive foods in miso soups and miso stir-fries might also play an important role in these findings (World’s Healthiest Foods).


This is the whole soybean and can be a delicious addition to an Asian-inspired dinner – every once in a while. Unfortunately, edamame is not fermented, so many of its anti-nutrients remain.

To summarize, quality and moderation are the key concepts when it comes to soy. And the less processed, the better.

Here is a tempeh-based recipe we provide at Ceres. Enjoy!

The tempeh we use comes from Alive and Healing, a great local brand in Sonoma County

Tempeh Treats (4 servings)

• 16 Ounces tempeh

• 3 Tablespoons extra virgin olive oil

• 2 Tablespoon balsamic vinegar

• 1 tablespoon miso

• 1 tablespoon fresh minced ginger

• 2 teaspoons minced garlic 

1. Cut each piece of tempeh into 3/4" cubes. Steam the tempeh for 6 to 8 minutes. Cool and place in a mixing bowl.

2. Whisk together the remaining ingredients, then pour the marinade over the tempeh. Marinate for at least an hour and preferably overnight.

3. When you are ready to cook the tempeh, saute it in a bit of olive oil until it is golden brown. Add the marinade at the end and stir well to coat the tempeh completely. Cool.


1. World’s Healthiest Foods. George Mateljan Foundation. Retrieved from:

2. U.S. FDA. Select Committee on GRAS Substances (SCOGS) Opinion: Soy protein isolate. Retrieved from:

3. Institute for Responsible Technology: genetically Engineered Foods May Cause Rising Food Allergies. Retrieved from:

4. Norris, Jack RD. Soy: What's the Harm? March 2011. Retrieved from: