In Defense of Legumes

This post was the inspiration for a chapter in my best selling Essential Thyroid Cookbook

You may remember earlier in the summer, I wrote a post called, AIP for Autoimmunity: Is it ALWAYS the Answer? where I explained that:

  1. I see merit in the Paleo and AIP (autoimmune protocol) diets right out the chute – in some circumstances.
  2. I’m wholeheartedly skeptical of removing whole food groups from the diet, even for those with autoimmunity.

I then followed that up with a spotlight on grains with a post called In Defense of Grains, where I explained that when you consider that properly prepared grains encourage the growth of friendly intestinal bacteria, help to keep the colon clean, and are high in antioxidants, we have to ask ourselves if moderate consumption of whole grains, along with a gut-healing protocol, is really such a bad idea.

Today, I want to round things out with a post about the benefits of beans/legumes.

My cookbook co-author, Lisa Markley, MS, RDN, and Bastyr-trained Culinary Nutritionist, and I don’t believe that beans/legumes are categorically bad for everyone, even during immune modulation and especially after your Hashimoto’s/autoimmunity is managed.

[Now available: the #1 best selling cookbook, The Essential Thyroid Cookbook: Over 100 Nourishing Recipes for Thriving with Hypothyroidism and Hashimoto’s.]

And just like I said with our grains post:

  1. Yes, this flies in the face of everything we’ve been told.
  2. Yes, we’re outliers – we’re totally sticking our necks out on this.
  3. I believe that too many have fallen prey to the slippery slope of what my functional medicine doctor calls, “being a prisoner of perceived risk.” In other words, there are many foods that may not be “risky” and he also doesn’t advocate a long-term, super-restrictive diet – for any autoimmune condition. Being a prisoner is stressful. And stress is a trigger for autoimmunity.

[Lisa and I recognize there are varying therapeutic diet approaches in the Functional and Integrative Nutrition communities that support thyroid and immune health, so our cookbook features user-friendly icons to help you easily decipher which recipes will fit your individual dietary needs at-a-glance. There’s no one-size-fits-all way to make our recipes work for everyone, so we made every effort to provide sensible adaptations to modify them to fit dietary practices such as Paleo and AIP, whenever possible. In most cases, the adaptation may include simply omitting an ingredient or making a simple ingredient swap to make it compliant.]

In Defense of Legumes
At the onset of the popularity of the Paleo/ancestral diet, it was widely reported that our ancestors didn’t eat legumes/beans/pulses and therefore we shouldn’t. But research has since found this to be incorrect – there’s evidence that hunter-gatherer groups did, in fact, consume legumes.

Similarly to grains, legumes contain the anti-nutrients phytic acid and lectin, which can compromise the integrity of the intestinal wall. But no one eats raw beans or legumes – and cooking has been shown to inactivate lectins. Additionally, lectins are found in over 50 fruits and vegetables, so steering clear of lectins is impossible if you’re eating a healthful, whole foods diet.

As for phytic acid, several foods are significantly higher in this anti-nutrient than legumes, including spinach, Swiss chard, sesame seeds, walnuts, and almonds. While a diet high in phytic acid can lead to mineral deficiencies, in the presence of healthy gut bacteria, we can break down phytic acid relatively easily, so there’s no good reason to remove these foods from the diet. (Just as with grains, soaking nuts reduces a significant amount of the phytic acid.)

The nutritional benefits of legumes are too far-reaching to ignore. They’re an affordable source of plant-based protein, they’re loaded with antioxidants, they’re an excellent source of energy-producing B vitamins that help to counter fatigue, they’re loaded with satiating fiber that can help with weight and blood sugar management, and last but not least, they help to naturally lower cholesterol, commonly elevated in those with hypothyroidism.

Beans/legumes are a primary protein source for vegetarians and vegans. Those who don’t eat meat, fish, or eggs have to get their protein some way, if for no other reason than to keep their blood sugar stable – balancing blood sugar and insulin is critical in balancing thyroid function. (For more I information, I recommend my e-book, Balance Your Blood Sugar.)

Without legumes, which includes soy (a popular protein source for many vegans/vegetarians and one that I only recommend in fermented form, like tempeh and natto, and still in moderation), vegetarians/vegans are largely reliant on nuts, which can be problematic. Consuming too many nuts can pose its own set of issues by way of digestive distress and can thus exacerbate gut dysbiosis and Hashimoto’s – or any other autoimmunity.

Many vegetarians eat eggs, which are a great source of protein, but they’re often problematic for those with gut dysbiosis. Remember, food sensitivities are different from food allergies. The vast majority of sensitivities can be healed with the right gut healing protocol.

For these reasons and others, I’m not an advocate of not eating nutrient-dense animal proteins, but I’m also not anti-legume. Still, working with vegetarians and vegans who have autoimmunity is tricky territory, especially given that, again, protein is so stabilizing to blood sugar and that for those with hypothyroidism, limited protein in the diet can lead to limited T4/T3 conversion and inadequate tyrosine. Tyrosine is critical for proper thyroid function; the thyroid’s job is to absorb iodine and combine it with the amino acid tyrosine. It then converts this iodine/tyrosine combination into T3 and T4, our two primary thyroid hormones.

For my meat-eating clients, I tell them to never make legumes the sole source of protein for any meal, but for vegetarians, it’s the most dense protein they’re going to get. I still feel that legumes should be consumed in moderation, but it’s difficult to be “moderate” and get adequate protein if you eschew animal proteins and you’re on a gut-healing program.

Similarly to grains, I believe that being legume-free long-term may be challenging for many people, vegetarian or not. Although many will argue (and I agree) that being grain-free long-term would be more difficult than long-term avoidance of legumes.

Lisa and I are not alone in our belief that moderate amounts of gluten-free, whole grains and legumes/beans can be part of a healing diet for those with autoimmunity.

Dr. Susan Blum, author of The Immune System Recovery Plan, regularly mentions quinoa, amaranth, millet, teff, buckwheat, various types of rice – and legumes – as part of her healing program and uses these foods in several of her recipes. She calls them “foods to include.”

She recommends legumes as a quality plant-based protein and explains how beans are a good source of glutamine, “…an amino acid that’s critical for healing leaky gut syndrome because it is the most important food for the cells that line the intestines.” Dr. Blum also claims that vegetarian protein in the form of lentils and beans is an important part of a “medically sound detox program.”

Similarly, Donna Jackson Nakazawa, author of The Autoimmune Epidemic, who healed from a paralyzing autoimmune disease, agrees that moderate amounts of non-gluten grains and beans help to “quiet down autoimmune activity” and espouses the powerful antioxidant activity of beans and legumes.

Natural health expert, Dr. John Douillard, states, “Beans [have] been found to protect the brain from cognitive decline as we age and have repeatedly shown to be one of the most protective foods against blood sugar concerns and cognitive decline. [They] provide an excellent source of proteins, fiber, minerals, and vitamins. While fiber is linked to heart health, it is also critical for the protective health of the intestinal skin. If the intestinal skin breaks down, the beneficial gut microbes disappear.”

Like grains, many experts claim that legumes improve digestive health by way of their prebiotic or “functional food” activity because they promote the growth of good bacteria. Justin Sonnenburg, PhD and Associate Professor of Microbiology and Immunology at Stanford is the author of The Good Gut, co-authored by his wife, Erica Sonnenburg, PhD. They’ve been trailblazers in researching how the fiber in grains and legumes improves the health of our gut microbiome, our 100 trillion organism-strong “mini ecosystem” also known as “the forgotten organ.”

They’re considered some of today’s preeminent experts in digestive health and state, “Over the course of studying the microbiota our family has adjusted what we eat to maximize produce and legumes, largely for their prebiotic content.”

For these reasons, some of Lisa’s recipes contain beans/legumes – and grains. But we’ve attempted to cover everyone with some adaptations and modifications – the recipes are written and keyed with flexibility to be adapted to various dietary approaches (Paleo, AIP, vegan). 

[This post contains affiliate links.]


I think I can breath for once after 1 and 1/2 years of avoiding gluten, soy, dairy, grains and legumes. I have hashimotos and was influenced by Dr Terry Whals book. I also live in Germany and finding a functional doctor has been a challenge so I depend on several reliable on line sources for my healing: Dr Izabella Wentz, Suzy Cohen, Dr Hyman and you...this news gives me hope. I find eating meat and nuts so boring and belive me I have tried a lot of things to make them unique. Beans or rice once a week might help drive my creative cooking desire! Thanks for the info and great resources.

Hi Melinda! I live in Mallorca, Spain. I buy my tablets for Hashimoto's in  Klöesterl Apotheke, Zurich. They make them from pig's thyroid.I have given up gluten but I haven't dairy. How can I know wether I have to give up dairy or not?

Thank you. Ana.

Hello Ana! I do not have allergies to gluten soy or dairy. I have sensitivities and decided to stop them all after much reading. I went from 175 mg of thyroid meds to 50 in 3 months when  stoppped eating gluten, soy and dairy. This was radical and I felt better. Try it for 3 months and see what happens. Seee how you feel and especially if it effects your dose. Good luck!

Hi Melinda. How did you find out you had to give up not only gluten but dairy also. I wonder wether I should give it up or not. How can I find out?

Kind regards. Ana.

Thanks for this well written and informative post.  I've long questioned Paleo's view that legumes are so detremental when you consider what other cultures eat (thinking Blue Zones).  I'm only at the beginning of my Hashi journey and though I'm told my thryoid looks like 'Swiss cheese', I feel certain that I can improve my situation to at least get off my low dose of Levo. 

I'm so conflicted with so much information. I have been vegetarian almost my entire life, with beans and lentils being a primary source of protein along with eggs, hardly any soy, and I have Hashimotos! My antibodies are very high. I hope I made the right decision incorporating more animal protien into my diet with AIP.

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