Dear Mark: What’s With The Bean Protocol?

bean protocolFor today’s edition of Dear Mark, I’m answering a reader question about beans. But it’s not just about beans. It’s about something called the Bean Protocol, a rather new dietary approach that many of my readers have expressed interest in. The Bean Protocol is supposed to improve the liver’s ability to clear out toxins, thereby preventing them from recirculating throughout the body in perpetuity. Today, I’m going to discuss where it fits in a Primal eating plan.

Let’s go:

Hi Mark,

Have you heard about this “Bean Protocol”? From what I can tell people are eating tons of beans and getting great results. It’s supposed to remove toxins from the liver or something else that only beans can do.

What do you think?



I did some digging around. I read the Bean Protocol coverage over at PaleOMG, where Juli has been following the protocol for several months now and seeing great results. There’s a Bean Protocol E-course that I did not sign up for, but I think I have a decent handle on the topic.

How to Do the Bean Protocol

Here’s the gist:

  • No caffeine
  • No sugar
  • No dairy
  • No gluten
  • No processed food
  • No factory-farmed meats; no fatty meats
  • Eat 6-8 half-cup servings of beans or lentils a day.
  • Fill the rest of the food with lean meat, leafy green vegetables, alliums (onion, garlic, leek, etc), and cruciferous vegetables (broccoli, cabbage, cauliflower).

What’s Supposed to Happen on the Bean Protocol

The soluble and insoluble fiber in the beans binds to toxins which the body can then flush out more easily. Without the fiber from the beans, your body can’t process and excrete the toxins, so they simply recirculate, stay in the body, and sometimes express themselves in the form of acne and other diseases. Adherents credit the bean protocol for fixing longstanding issues like acne, Crohn’s, and many other conditions.

Bored with beans? We have 41 ways to make them more fun. 

Is this true? Is there any evidence of this in the scientific literature?

Well, there isn’t much direct evidence for beans improving liver clearance of toxins, but there is circumstantial evidence. For one, prebiotic fiber is good for liver health. There are plenty of studies to support this.

Synbiotics (a combination of probiotics and prebiotics) and BCAAs taken together improve hepatic encephalopathy, a feature of liver failure where the liver fails to detoxify excess ammonia.1 However, it does not do so directly. The fiber isn’t necessarily “binding” to the lead and excreting it. Instead, it does so by increasing levels of lead-binding gut bacteria which in turn bind and excrete it, shoring up the gut lining so that lead can’t make it into circulation, increasing bile acid flow, and increasing the utilization of healthy essential metals (like zinc and iron). The bacteria are essential for the effect; pre-treatment with antibiotics abolishes the benefits. So we can’t say for sure that the fiber itself is “binding” to the toxins.

Allium, Inulin

The Bean Protocol is also rich in allium vegetables like garlic and onions, another source of prebiotic fibers shown to improve liver health and toxin clearance. For instance, inulin given to rats prevents acute cadmium toxicity.2 Inulin also increases bile flow.3 Moreover, compounds found in garlic improve glutathione activity in the liver and enhance its ability to metabolize toxins.4

Cruciferous Vegetables

The Bean Protocol also emphasizes cruciferous vegetable consumption. The crucifers, which include cabbage, broccoli, cauliflower, and kale, can exert beneficial effects on liver health. Sulforaphane, one of the most prominent compounds in cruciferous vegetables, has well-established effects on toxin clearance. It can speed up the clearance of airborne pollutants and counter the carcinogens formed from high-heat cooking.56

Back to Basics

By emphasizing lean meats and eliminating sugar, alcohol, and industrial food, you are eliminating the major causes of fatty liver in the diet: sugar, seed oils, and alcohol.

My point is not to disparage the Bean Protocol. I think it has some merit. My point is to point out that beans alone probably don’t explain the benefits people are seeing. There’s a lot more going on than just beans.

Lectins and Phytic Acid in Beans

Okay, okay. So while beans aren’t the only (or even necessarily the best) way to obtain prebiotic fiber to modulate gut bacteria and improve liver health and therefore toxin clearance and metabolism, they are promising. But aren’t beans bad for you? Aren’t they neolithic foods full of lectins and anti-nutrients that are anything but Primal?

Lectins are anti-nutrients and beans do have them. Studies show that they can damage the intestinal lining, prey upon already-damaged intestinal lining, and prevent the body from repairing that damage.7 If they make it into the bloodstream, they can bind to cell membranes throughout the body, trigger autoimmune reactions, and cause real havoc.8 People have actually been hospitalized from lectin poisoning.9

But here’s the thing: cooking and soaking deactivates the majority of legume lectins.

  • In one study, navy and kidney beans showed 0.1% lectins leftover after cooking.10
  • One study found that pressure cooking kidney beans for 30 minutes eliminated all hemagglutinin activity.11
  • In another, a combo of soaking and cooking white beans completely eliminated activity of the most pernicious lectin, the one responsible for kidney bean poisoning: phytohemagglutinin.12

Most of the research indicting legume lectins used animals consuming large amounts of raw lectins. Those people who got lectin poisoning ate undercooked kidney beans. Don’t eat raw or undercooked beans and make sure they’re soaked overnight. Canned beans are also prepared pretty well.

Okay, what about phytic acid?

Phytic acid is the primary storage form of phosphorus in plants. When you eat a food containing phytic acid, it can bind to several other minerals, like calcium, magnesium, and zinc, and prevent their absorption. Diets based entirely in high-phytate foods can thereby lead to nutrient deficiencies. As legumes are one such high-phytate food, people are justifiably cautious about basing their diet on them.

Soaking legumes is really good at reducing phytic acid. In one study, cooking straight up without soaking reduced phytate by 20%, cooking after soaking in the soaking water reduced it by 53%, and cooking after soaking in fresh water reduced it by 60%.13 Another study found that cooking in fresh water after 16 hours of soaking with a 3:1 water:bean ratio eliminated 85% of phytate.14 That basically takes care of the problem.

If you want to really eliminate phytic acid you can sprout your legumes. You can also buy pre-sprouted beans.

What about the carb content of beans?

Legumes are higher in carbs than many other Primal foods but not as high as you might think. The musicality of the legume partially offsets its carbohydrate density. All those sugars and fibers being digested by gut bugs and producing the farts are carbs that you aren’t consuming as glucose. If you pay attention to “net carbs,” you’ll love legumes—at least compared to something like potatoes or bread.

Which, by the way, is why legumes appear to be so helpful in the Bean Protocol.

A half cup of cooked black beans has 20 grams of carbs with 7.5 coming from fiber.

A half cup of cooked chickpeas has 30 grams of carbs with 5 coming from fiber.

A half cup of cooked pinto beans has 22 grams of carbs with 7.7 coming from fiber.

A half cup of cooked lentils has 20 grams of carbs with 7.8 coming from fiber.

And much of that fiber, remember, comes in the form of galactooligosaccharides, that same prebiotic shown in studies to improve gut health and even increase lead excretion. But these are also FODMAPs, which, depending on your gut biome, can be helpful or painful. Some people won’t be able to handle the gas, some will get downright painful bloating, while others will get huge prebiotic benefits. Your mileage may vary, so just figure out what works.

Are beans actually nutritious, though?

Legumes aren’t nutrient-dense compared to something like liver or oysters, but they’re more nutrient-dense than grains and many other foods.

Again, a half cup of beans isn’t very many carbs. Maybe 20 grams, with only two thirds of that turning into glucose. You’ll get a lot of food for your gut and a decent whack of some important nutrients like folate, copper, magnesium, and manganese. That half cup of black beans provides 32% of your daily folate requirements, 20% of copper, 14% of magnesium, and 17% of manganese. A half cup of lentils provides 45% of your daily folate requirements along with 28% of copper and 21% of manganese. Not bad for a measly 20 grams of carbs.

A Plea: Lentils

If you want to try the Bean Protocol and insist on doing the 8 servings a day version, I’d recommend you go with lentils.

A cup of standard lentils gets you:

  • 40 grams carbs, almost 16 g fiber.
  • 230 calories.
  • 18 grams protein. Legume protein can’t replace animal protein, but it can offset some of your requirements.
  • 90% of folate.
  • 28% of vitamin B1 (thiamine), 25% of vitamin B5 (pantothenic acid), and 21% of B6 (pyridoxine). B vitamins generally aren’t issues for folks eating Primal, but they can’t hurt.
  • 55% of copper.
  • 17% of magnesium.
  • 43% of manganese.

Lentils added to a meal slow gastric emptying, which should keep a person fuller longer.15 This is in contrast to most sources of refined carbs, which increase a person’s hunger.

Another benefit is that lentil prep is simple. They contain less phytic acid than most other legumes and require less soaking (or none at all) and cooking time than other legumes to reduce it. If you want to sprout lentils, they sprout much quicker than beans.

All in all, I’d say the Bean Protocol is worth trying if you’re interested or intrigued. I don’t know that the “8 servings of beans” is more important than the other stuff you’re eating or omitting, but I also know that sometimes things just work a certain way even if the hard clinical evidence hasn’t been established. After all, people used to say the same thing about Primal or keto.

If you do try out the Bean Protocol, be sure to keep us all informed and up to date on your progress. I’d be really curious to hear about it.

TAGS:  gut, toxins

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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35 thoughts on “Dear Mark: What’s With The Bean Protocol?”

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  1. It feels like you could make an “anything protocol” as long as it involved cutting out grains, sugar, and seed oils, and people would rave about the health benefits of the carrot protocol or the meat protocol or the potato protocol or whatever else. It’s almost like you’re 80% of the way there if you eliminate those foods. Maybe we should call it something like “eating primally.”

    1. It does, and I think that’s a great thing. Some people just enjoy the taste of beans; if this is what it takes to make them healthier (and we all know that we descend a deep rabbit hole when we start thinking from a health perspective), more power to them.

      An industrious mind might try to figure out those different staple foods that different people enjoy (rice, corn, wheat, shellfish, etc.), or even vices like alcohol or marijuana, and adapt this model to suit. It may be a little dishonest, but motivation is motivation. If it’s a net positive change, why not?

    2. I agree that cutting out the junk is probably a big part of healing. But If you follow PaleOMG, she has had great success with her acne on the bean protocol. And she had been eating Paleo, cut out sugar and all the other things for years before trying the bean protocol. She claims it’s the beans that helped her.

    3. This is actually about detoxing by decreasing the amount of bile that is reabsorbed into enterohepatic circulation and increasing the amount of bile – and toxins – that are excreted. For that you need soluble fiber and beans are natures answer.Of course, it is also about limiting the junk going in as well. If you are not having any health issues and are not looking to enhance your detox mechanisms, then don’t do it.

  2. I like beans. I know they aren’t officially “primal” but no one has convinced me they aren’t good for you.

    Why not just incorporate properly prepared beans and lentils into an otherwise unprocessed diet, instead of setting yourself up for the gut misery of suddenly expecting your body to process large amounts of a food it isn’t used to?

    When you eliminate that many things from your diet at once, it’s hard to give beans the crown for being the sole source of anything good that happens.

  3. I don’t quite get the idea of toxins circulating in perpetuity. Much of the cleanse culture seems to think that there are ways to speed up or hyper intensify the body’s waste removal..and no doubt, there are probably a variety of ways to make it more efficient. But, what I’ve come to understand is that our physiology is predisposed to eliminate harmful items in a default way. Sure, there are many such as heavy metals that our “ancestral programming” isn’t so equipped to handle, but I can’t see how legumes are the antidote to that chronic circulation of those harmful items. I guess that I’m with Mark on this, that the ancillary tenements of the protocol are probably what are responsible for the detoxification benefits.

    1. To simplify it, soluble fiber aids in detoxification by binding to bile in the intestines, which makes it resistant to reabsorption via enterohepatic circulation. 95% of bilirubin is reabsorbed. Beans have a high amount of soluble fiber. It is recommended to eat a couple of tablespoons in between meals – or eat them without fats, like olive oil, that would also bind to the fiber and compete with the bile. If you are healthy and not working on any specific health issue, you’d be fine just increasing your intake along with a variety of fiber rich foods.

      Maybe Mark should’ve mentioned enterohepatic circulation…. or taken that e-course.

  4. That protocol is 160 g of carbs a day… I’m not sure how you can deviate so far from Primal or keto to suggest that this is something you followers should do. It feels like you’re trying to capture a ‘market’ for your products by appealing to people that like carbs. It feels like you’re selling out and I, for one am disappointed at where your ‘primal’ philosophy has gone of late.

    1. Oh jeez… Mark received several reader questions (including my own) about his take on this protocol and whether or not it has any merit. He simply answered our question with his honest thoughts. It is nothing new at all for Mark to suggest legumes aren’t that bad and may offer benefits to those who can handle them. The whole Paleo movement in general changed their stance on legumes a while back. He isn’t endorsing this protocol or at least not by anything I can tell from reading the article…

      1. The whole movement except Dr. Loren Cordain. I don’t think he’ll ever change his stance on legumes.

        It was pretty shocking when Sisson embraced keto. I never expected to see keto bread recipes on this blog. But, that’s the great thing about Sisson’s blog. He’s not confined to a dogmatic dietary approach. He follows the science.

    2. Also all of Mark’s products are low carb, so I don’t understand how you came to the conclusion that he’s trying to appeal to people who “like carbs”. (But seriously, doesn’t almost everyone like carbs in some form?)

  5. Anyone who treks in Nepal is amazed by the strength and endurance of the wonderful porters and guides. As far as I could tell, their preferred diet is dal bhat–lentils and rice. A possible trade off is that, until recently, the country had a very low life expectancy.

    1. yes, all that with an EXTREMELY high level of ghee in their dal and then their blood….they eat a LOT of ghee (and lamb and goat) over there….
      in fact Nepalese dal is my favorite form of dal–it is so much richer than that of other areas…

  6. If I ate 6 to 8 cups of beans/lentils a day, along with alliums and cabbage, I’d probably explode into a black cloud of noxious gases. (Has anyone considered the fart factor with this diet?) I like beans, but only periodically, and I don’t OD on them.

    1. What are some good prebiotic sources for those of us that hate beans and lentils? I don’t like cabbage either.

    2. Best way to get rid of that gas is to bring the beans to a boil, boil 2 minutes, turn off the heat, soak for an hour, then rinse and throw away the rinse water. Add fresh water and cook as usual Gets rid of the overwhelming majority of oligosaccharides.

    3. Your body normalizes to the point where they won’t effect you. Start slowly and build up if you are not a regular consumer of beans.

  7. Just a small amount of beans leaves me in distress for days. No thanks. I’ll keep getting my prebiotics elsewhere

  8. It sounds fairly similar to Tim Ferris’ Slow Carb diet except he advocates for a cheat day and allows a few other foods.

  9. I agree that this is so much more than the beans…it’s all the things that are being eliminated. But after all the beans I ate as a vegetarian I do not miss them at all. I don’t bother to prepare lentils anymore, but would definitely consider adding them in from time to time. I also used to sprout them from time to time…really great in a salad and easy to do.

  10. I’m just thrilled “Dear Mark” is back! Love these posts! More Dear Mark please Mark, so great to hear your perspective on any diet and health related topics.

    I have been incorporating more beans and legumes since covid hit (quality meat in my country due to the restrictions has been harder to find) So I was very interested in this article.

    I’ve actually found I personally feel better with less fatty cuts of meat and more high quality natural carbohydrates. I was resistant to this shift as I know how nutritious animal based fats are- but I actually feel better with a low fat way of eating which baffles me (Truly low fat, probably less than 10% of my overall diet)

    I eat a lot of beans, sweet potato, fruit and vegetables and occasional low fat white fish and oysters (easiest quality animal proteins to get where I live) and am feeling much better than I did when I ate a higher fat diet. My skin nails and hair have all improved and my energy level.

    It’s been an unexpected shift, I will continue of course to monitor how I feel and what I’m drawn to as more options become readily available again (pastured ethical meats etc)

    Also, as a follow up to this for your next “Dear Mark” could you comment on my above diet and give insight into why I could possibly be thriving on this compared to a more meat heavy highs fat one? I find it bizarre myself!

    I’m a young female who has always been lean, probably too lean, and also have Ulcerative Colitis (another reason I’ve usually stayed away from a fiber filled plant based way of eating)

    Thank you so much Mark and please continue to post “Dear Mark” 🙂

    1. Oh my goodness I wish I could remember the title of the article or the author, but I believe Mark linked to it in one of his past Link Loves, it explained low fat high carb diets and so many studies that support their healing properties, etc but only under around 10% fat I think, as you are doing. It was very extensive. I think it was written by the woman who wrote the popular article debunking the China study.

  11. Another super post. My two cents is that eight cups of beans is a tad much. I think sprouted lentils are the way to go along with some black beans, not kidney beans

    If lentils are problematic for one, I would swap in adzuki beans. Easy to cook, as long as you soak them and cook them in fresh water. Adding some organic whole grain rice to the mix of lentils or beans makes for a better amino acid profile I have read.

  12. Read the article! It says 6-8 HALF-CUP servings of beans, not 6-8 cups of beans. Big difference.

  13. Not sure why my comment was deleted but this article isn’t completely accurate. If you want to know about The Bean Protocol it’s best to speak with Karen Hurd or Unique Hammond. The amount of beans eaten varies based on what your specific needs are and no one is eating 6-8 cups or even half cups per day, especially not in the beginning.

  14. I have researched canned beans and it looks like in their processing they are pressure cooked, so in terms of convenience, they are winners.
    They have a lot of sodium, but otherwise they should be good to go.
    Does anyone know anything else?
    Thank you.

  15. I’m on the bean protocol and want to point out that the bean servings are based on weight and why you’re on the protocol. You eat 1/4-1/2 cup of beans 3-6 times per day to total 1 1/2 cups per day not 6-8 1/2 cup servings which would be 3-4 cups per day.

  16. I’m not promoting the bean protocol, just typing what I know about it.
    They don’t want you to sprout beans. You can soak them over night but not sprout them. Sprouting turns the soluble fiber into insoluble. In the bean protocol you want all the soluble fiber you can get.

  17. This was a great response. I am a certified primal coach and what I love most about Mark Sisson is that he is not dogmatic about being paleo/primal. He’s about health and science. It’s why I’ve loved his teachings over the last 12 years. Thank you Mark for all you do.