If you enter our kitchen today, you won’t find many legumes. Like many others who stick to Paleo-style diets, we keep legumes (except for fresh, green peas) off of our menus. However, science and research is always changing, and we continue to learn about the best ways to nourish our bodies. Some Paleo practitioners have softened their stance about avoiding legumes, while other ancestral dietary programs have always included beans. As we’ve said before, dietary choices are all about choosing your best fuel for your own personal biochemistry. Those who are in the process of healing their gut and those with autoimmune disorders may not be able to tolerate legumes. Those with healthy guts and immune systems are less likely to have trouble, especially when the legumes are properly prepared. Still, it is important to remember that legumes are not nearly as nutrient-dense as other animal sources of protein.

Some legumes, like lentils or dal, contain fewer problematic compounds and are easier to digest than heartier legumes like kidney and lima beans. Green peas and snap peas also tend to be more successful. However, there are a couple of legumes—peanuts and soy—that we try to avoid. Unless you are particularly sensitive, peanuts can be fairly easy to avoid. Soy, on the other hand is a bigger challenge. Below, we’ve laid out some tips for phasing soy out of your diet.



Soy products are problematic for multiple reasons. They’re allergenic, they’re high in antinutrient defensive compounds, and they’re frequently genetically modified. We try to stay away from soy in our kitchen. But soy products are everywhere, and it can be challenging to phase them out. Here are some tips for reducing your soy intake:

Skip substitutes: Processed soy protein finds its way into all kinds of foods these days — it can be used to make “chicken” nuggets, milk, and even egg-free mayonnaise. But these products are a far cry from the original bean, and they often come loaded with preservatives in addition to the antinutrient factors already present in soy. If you need to eat plant-based protein, try sprouted lentils. For non-dairy milk, try homemade almond or coconut milk. Avocado makes a great replacement for mayonnaise if you can’t or choose not to eat eggs.

Try to get protein from whole foods: Protein powder and protein-enhanced energy bars are  popular choices for athletes and gym rats, but they is often made using processed soy protein. This isolated soy protein is frequently made from a byproduct of soy oil production, which goes through several processing steps that add additional harmful compounds. Instead, pay attention to the protein levels in your daily meals. If you find that you cannot get enough protein from meat and dairy alone, talk with your health practitioner about the best way to increase your protein soy-free.

Scrutinize labels: Soy can hide just about anywhere. Soy lecithin, protein, isolate, flour, and concentrate are easy to spot on labels, but you should look out for hydrolyzed plant protein and hydrolyzed vegetable protein as well. These ingredients are common in processed foods, so if you skip processed foods, you’ll be able to avoid these as well. Soybean oil lurks in most “vegetable oils” — we don’t recommend cooking with these at all.


Legumes are controversial ingredients in ancestral-based diets. Some, like the Weston A. Price Foundation, recommend eating legumes on a semi-regular basis, while others, like those who follow Paleo- or Primal-style diets, often stay away from them. Why?

Legumes are seen as having high levels of antinutrient factors. These factors include digestive enzyme inhibitors, phytic acid, and flatulence-promoting oligosaccharide carbohydrate chains. While relatively high in protein, B vitamins, and essential minerals like magnesium and potassium, legumes are less nutrient-dense than most animal products, and therefore not a necessary food in any well-balanced omnivorous diet.

On the other hand, many of the antinutrient factors can be eliminated via sprouting, soaking, and long, slow cooking. Legumes are a cheap source of protein for those on a budget, and when cooked properly and eaten as a supplement (not a substitute) to more nutrient-dense foods, they are safe to eat for those who are not sensitive. Remember, the most important consideration is your own individual biochemistry. If you’re experimenting with legumes, pay attention to your digestion. Bloating and gas are signs that the legumes either haven’t been prepared properly or that you can’t tolerate them.

Certain legumes are better to eat than others, so it is worth diving deeper to explore the science behind the bean.

What’s a legume anyway?


Legumes are all members of the plant family Fabaceae, which is the third largest flowering plant family. Legume plants are grown for food (in which case they’re often called pulses), livestock forage, industrial oil production, and soil enhancement. Legumes have two to three times the protein content of cereal grasses, and are notable for their unique ability to fix nitrogen from the air into the soil.

The first legumes were likely cultivated in the Middle East. Today there are around 20 common species eaten around the world. Soybeans and peanuts, which are both cultivated for their oils in addition to the whole bean, far outpace other legumes in the scale of their production. Chickpeas, lentils, peas, fava beans, and alfalfa are native to Europe and the Middle East; soybeans, mung beans, black gram, azuki bean, and the pigeon pea are native to India and Eastern Asia; black-eyed peas and groundnuts are native to Africa; and the common bean, lima bean, tepary bean, runner bean, and peanut are native to the Americas.

We most often eat the seed of the legume plant, and it is structurally similar to other seeds and grains. Each legume consists of an embryo and a protective seed coat. The embryo’s nutrient storage center is called the cotyledon — it’s the creamy center of the cooked bean. The cotyledon is made up of mostly protein and starch, except in the case of peanuts and soybeans. These two legumes have a very high fat content in addition to protein and starch. Some legumes, like peas, contain significant levels of sucrose, and they taste distinctively sweet once cooked.

Depending on the species, legume seed coats can be very thin, like a peanut, or as much as 15% to 30% of the legume’s weight. Chickpeas, for example, have a thick, tough seed coat. The seed coat is made up almost entirely of carbohydrates, and is the primary source of the legume’s indigestible fiber. Colorful seed coats, like those of the cranberry bean, get their vibrancy from antioxidant anthocyanin pigments and phenolic compounds. These compounds are often leached out into the cooking water, so if you’re cooking these beans, be sure to keep the cooking liquid!

What’s the problem with legumes?

Like other seeds, most legumes are high in defensive compounds. These defensive compounds (or antinutrient factors) protect the seed from germinating or sprouting until the conditions are right for growing into a new plant. They resist digestion once the legume has been eaten, and they can cause digestive distress and poor nutrient absorption if the legumes are not properly prepared.

The two most common defensive compounds found in legumes are the enzyme inhibitors and the lectins. Legumes contain both protease enzyme inhibitors and amylase enzyme inhibitors. They prevent the enzymes that digest proteins (proteases) and starches (amylases) from breaking down large molecules into smaller, easier to absorb amino acids and sugars. Lectins are large proteins that can also interfere with digestion. Legumes contain relatively high amounts of the lectin agglutinin, which is found in the highest levels in soy, kidney, and lima beans. These can bind to intestinal cell walls, preventing them from absorbing nutrients. Because they are large and difficult to digest, agglutinins are also capable of moving through the gut wall, entering the bloodstream, and triggering an immune response. Both enzyme inhibitors and lectins can be inactivated by soaking the beans and by cooking them for a long time over low temperature.

Phytic acid is another defensive compound found in legumes. Phytic acid binds to minerals in the legume to form phytates. When a mineral is bound up with phytic acid, it cannot be absorbed in the body. Our digestive systems have a very difficult time breaking down phytates, which means that we often don’t absorb the minerals in legumes. Sprouting legumes before cooking them will free the minerals from the phytic acid, making them absorbable by the body.

The other common problem with legumes is that they contain carbohydrate molecules that are impossible for our digestive enzymes to break down. These compounds are then transported to our lower digestive system, where our gut bacteria feast on the sugars in the carbohydrates and produce gas. This gas is then expelled as flatulence. Oligosaccharides in the cotyledon and the compounds that hold together the legume seed coat are both hard to digest. Beans with thicker seed coats will often create more flatulence than those with thin seed coats. Soy, navy, and lima beans are particularly problematic.

While all beans contain some level of these defensive compounds, some have higher levels than others. Lentils, mung beans, and black gram (or urad dal) are all relatively low in all defensive compounds. They also have thin seed coats and therefore contain fewer flatulent compounds. If you choose to experiment with legumes, these are good places to start.

In order to make the nutrients in legumes as bioavailable as possible, sprouting and/or soaking them before cooking is necessary. You can find a good guide to sprouting here. Once they’re in the pot, cook them low and slow. The cooking liquid should remain at a gentle simmer (keep the heat on low). Depending on the legume, they will take anywhere from 30 minutes to 2 hours to cook. Because some of the nutrients will be leached out into the cooking liquid, it is best to cook legumes in as little liquid as possible. Save any cooking liquid and serve it in the dish.

The problematic pair: Peanuts and Soy

While current research shows that many legumes can be tolerated by robust individuals if prepared correctly, there are two that are highly problematic and best avoided: peanuts and soy.

Peanuts: Although they are commonly eaten and referred to as nuts, peanuts are actually members of the legume family. As we mentioned above, peanuts are notable for their fat content compared to other legumes. (They are about 25% oil by weight.) Peanuts are also relatively high in protein. In America, they are most often served roasted and salted or else roasted and churned into peanut butter. In certain places in the South, peanuts are served boiled in the shell.

Peanuts are considered to be some of the most highly allergenic foods. While the allergy only affects between 0.6 and 1% of the American population, this number is on the rise. Many peanut allergies cause anaphylaxis, which is a rapid reaction resulting in rashes, hives, the swelling of the throat, cardiac arrest, and low blood pressure. Anaphylaxis can be fatal if not treated quickly.

Peanut allergies occur when the antibody immunoglobulin E (IgE) encounters the peanut protein and releases histamine into the body. Histamine sets off a cascade of reactions, including the dilation of blood vessels and simultaneous constriction of the air passageways in the lungs. As of today, it is not known how someone develops a peanut allergy. Some believe that the increase in peanut allergies is correlated with the increase in soy milk formula, while others believe that the risk of allergy decreases depending on the number of peanuts the mother eats while pregnant. Still others cite the hygiene hypothesis — that is, we are more susceptible to allergies when we live in completely hygienic environments. Finally, some think that early exposure to peanuts can prevent allergies from developing. Clearly, more research needs to be done.

In addition to the allergy problem, peanuts are also highly susceptible to mold contamination. The primary mold that infects peanuts is the fungus Aspergillus flavus, which releases a potent carcinogen called aflatoxin. The risk of aflatoxin contamination is higher in lower quality peanuts and in those where visible mold is present. Peanuts are also highly susceptible to e. coli and salmonella bacteria; these can only be destroyed when roasted at a high enough temperature for long enough time.

Finally, when peanuts are roasted (as they most often are) they still contain all of the defensive compounds characteristic of legumes.

Soy: Soybeans were first cultivated in Asia around as an animal food and cover crop. The first evidence we have of humans eating soy as a food was in China around 200 BC. The Chinese had discovered that, by fermenting the bean into a funky paste, they could transform the difficult bean into a more nutritious accent to their food. This miso-like paste was called chiang, and the liquid that pooled on the top was the first known soy sauce. From there, the Chinese spread fermented soy to Japan, where they developed natto (fermented whole soybeans) and miso. Tofu was a later development made from coagulated soy milk. Tempeh was the final fermented soy product to be developed, and it first appeared in documents starting in the 1600s.

Regardless of their ingenuity, the Chinese and Japanese peoples typically ate soy products in smaller amounts or as accents to other meat-based dishes. The one exception to this rule is the Buddhist monasteries that began including tofu as a major source of vegetarian protein in their plant-based diets.

Besides tofu, all of these traditional soy preparations required significant fermentation. Long fermentation drastically improves soy’s digestibility and nutritional profile. The process transforms the chemical makeup of soy by using bacteria, fungi, and other beneficial microorganisms to break down the proteins, starches, and fats in the bean into more digestible amino acids, simple sugars, and fatty acids. The end result is a soy-based food with reduced phytate levels and increased bioavailability of riboflavin, niacin, vitamin B6, pantothenic acid, folate, and vitamin K. Like all other legumes, soybeans contain antinutrient factors, and these are deactivated by long fermentation.

It’s important to note that proper fermentation requires a significant time investment. Quality miso can take 3 years to make! However, many of these foods are now made at a rapid clip in modern factories — some soy sauces are made in as few as 3 days. These versions do not carry all of the benefits of the original and may retain defensive compounds. In addition, modern soy products are also eaten in high amounts. Traditional miso, natto, tempeh, and soy sauce are all very salty and are therefore hard to eat in anything but small portions.

Soy likely came to America in 1770 with the help of Benjamin Franklin. Despite his insistence that soy would be a boon for the new colony, soybeans did not become a major crop until the 1930s. By that time, soy’s abundant oil reserves had become clear, and the beans were grown primarily for industrial oil production. The protein-packed leftover pulp was originally used exclusively as animal feed.

Both Harvey Kellogg and Henry Ford were early adopters of soy; in fact, Ford was so infatuated with the bean that he developed car fuels, plastics, and even clothing from it. Indeed, as Kaayla Daniel writes in The Whole Soy Story, soybean production in the west is a product of the industrial revolution, “an opportunity for technologists to develop cheap meat substitutes, to formulate soy-based pharmaceuticals, and to develop a plant-based, renewable resource that could replace petroleum-based plastics and fuels.”

Today, manufacturers have found abundant new ways to profit from the excess soy pulp extruded during the oil production process. One of the most common soy oil byproducts is called soy protein isolate. It begins as crude, defatted soybean meal. To refine it for food use, the meal is first mixed with an alkaline solution to remove all of its fiber. Then it is washed in an acidic solution to precipitate out the protein from the meal. This protein is dipped into an alkaline solution to further refine it, and then it is spray-dried at high temperatures to turn into it into powder. This powder is used in many different product products like energy bars, protein shakes, pre-formed burgers, and hot dogs. Besides the fact that the entire manufacturing process introduces plenty of places for chemical cross-contamination, it also removes any beneficial nutrients from the soybean. All that is left is pure protein, plus the carcinogenic compounds lysinoalanine (a cross-linked amino acid that forms when the amino acid lysine goes through a strong alkaline treatment) and nitrosamines (a mutagenic compound that is produced from nitrates).

Of course, soy protein isolate is not the only soy product on the marketplace today. Shelf-stable soy milk, tofu, and vegetarian “meats” are all common items in today’s grocery stores. Soy sauce is as common of a condiment as ketchup. While some of these products do contain whole soybeans and are not made from the dregs of industrial oil production, very few are produced using the traditional methods of long, slow fermentation.

In addition to the production problem, soybean agriculture presents environmental concerns. At least two-thirds of the US soybean crop comes from genetically modified soybeans sold by Monsanto. These soybeans have been modified to be resistant to the herbicide Round-Up. This “Round-Up Ready” soy was originally billed as a crop that could be grown with fewer levels of pesticides. However, the frequent use of Round-Up can lead to the growth of resistant weeds, which then require application of additional herbicides. Overuse of any herbicide causes the soil to degrade. In addition, the monocropping culture advocated by companies like Monsanto contributes even further to the degradation of the soil. Increased demand for soybeans has exacerbated these problems, and has led to deforestation of large portions of South America.

So why do people even like to eat soy?

Compared to other legumes, soybeans have far greater nutrient density. They have double the protein content of other legumes, contain almost all of the essential amino acids, and they are rich in oils, isoflavones, phytosterols, and saponins, three compounds that are the source of both positive and negative physiological effects.

Isoflavones are phenolic compounds that are released with the gut bacteria digest soybeans. They are known as phytoestrogens because they resemble the hormone estrogen and therefore have hormone-like effects on the body. While some studies show that isoflavones can slow bone loss as well as the development of prostate cancer and heart disease, other researchers have found that they can worsen preexisting breast cancer, prevent ovulation, and accelerate hypothyroidism. A Harvard Public Health study showed that increased soymilk consumption by men can decrease sperm count, especially when they were overweight or obese. It is important to note that while fermentation can deactivate soy’s defensive compounds, it does not break down isoflavones. Fermented soy products, even high quality ones, will still contain this compound.

Phytosterols are chemical relatives of cholesterol that interfere with our absorption of cholesterol and lower total cholesterol levels. Not surprisingly, they are used to treat patients with high cholesterol. Like isoflavones, however, phytosterols are structurally similar to the hormone estrogen and can potentially cause hormone disruption.

Soybeans are also high in the defensive compound saponin, which gives soy its emulsifying ability. The saponin makes up around 5% of the total weight of the soybean, including the inedible hull. Saponins interact with cholesterol molecules in cell membranes to form pores in the cell. Some types of saponins are large enough to permanently damage the cell; others allow the pores to close and can increase mineral absorption.

If you do not have an allergy or intolerance to soy, eating small amounts of traditionally prepared products like miso and natto is likely not harmful. However, it is best to seek out those products that are made from 100% organic to guarantee that they are not made from GMO stock.