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  • Roxie Daggett

Best Instant Pot Black Beans (Carb Cycling, Digestion, MTHFR Support)

Updated: Nov 29, 2022

From black bean chili to hearty stews and tasty tostadas, black beans make nutrient-dense and crowd-pleasing recipes. They also work great for carb cycling and MTHFR gene support (details below), but they aren't always easy to digest. Let's take a look at the power behind this super bean and how to cook them and cycle them for optimal nutrition and digestion.

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This bean recipe is a deep dive into the incredible nutrient value of black beans and how they work with carb cycling and contribute to MTHFR gene support. It also includes 5 tips for optimizing bean digestion. Of course, feel free to jump to the recipe for creamy and delicious Instant Pot black beans, or navigate to the sections that interest you.

Black Bean Superpowers

Black beans have micronutrient superpowers. In fact, they could be considered a multivitamin of sorts.

They are loaded with a unique array of vitamins, minerals, antioxidants and anti-inflammatories that make your genes happy, fight off disease, and promote longevity.

One cup of cooked black beans contains about 64% of your daily folate (B9) needs which is important for DNA methylation (to support optimal gene activity). Black beans are also high in manganese, magnesium, thiamine (B1), phosphorus, iron, copper, potassium and zinc. They have small amounts of riboflavin (B2), B6 and calcium in addition to some niacin, pantothenic acid, selenium and vitamin A.

Black beans are also rich in the amino acid lysine which is though to have anti-viral and anti-cancer effects.

Lastly, all beans are a great source of fiber. Fiber is a wonderful and easy way to detoxify your body by just using food. Fiber stimulates optimal gut, liver and kidney function to help move toxins out of your body.

These humble legumes are packed with high-powered nutrition!

Black Beans, Blue Zones & Longevity

Beans or legumes, including black beans, are found in most of the Blue Zone diets which have been associated with longevity.

Black beans are eaten at nearly every meal on the Nicoya Peninsula in Costa Rica-- home to one of the world's largest populations of centenarians-- people 100 or more years old. Undoubtedly there are other factors at play in these locations, but beans are an ancient food that have sustained generations everywhere and continue to be a nutrient-dense staple across the globe.

And it's not just in the Blue Zones. There have been fascinating studies from all over the world associating beans with positive health outcomes and longevity. In this research, bean consumption has been correlated with health benefits such as:

Black Beans: Berry Good Antioxidants

Black beans are high in several antioxidants, especially anthocyanins, which are also found in dark berries and other blue foods.

My post, Top 20 Blue Foods For Your Pantry & Fridge (+ 5 Surprising Health Benefits) talks in detail about blue foods and the amazing benefits to eating anthocyanin-rich foods. There is one animal study that showed how anthocyanin-rich black beans prevented DNA damage during a chemical mutagen exposure! Interestingly, the study showed genetic damage to be WORSE when the mice were given anthocyanin as a commercial supplement, vs. feeding the them a partial black bean diet.

This research points to the importance of using whole foods for optimal health outcomes rather than relying on isolated supplements, in this case to prevent DNA damage. A big amen to that!

I always prefer a food first approach over taking lots of vitamins and supplements (even though I take them as an insurance policy since our soils are depleted of many nutrients).

Black beans fill the bill as a phenomenal source of essential micronutrients (vitamins and minerals) plus disease fighting compounds.

Black Beans & Your Genes: MTHFR Support

We all have about 20,000 known genes in our bodies. Science is teaching us more about specific genes with extremely important functions. One of those is called the MTHFR gene.

The MTHFR gene helps your body process certain vitamins-- namely folate (B9)-- which helps build, repair and protect your DNA through a process called methylation. This is why pregnant women are encouraged to take folic acid (a synthetic form not always processed by well by those with the MTHFR mutation) to prevent neural tube defects in the baby. The MTHFR gene also helps metabolize hormones and detoxify your body.

The MTHFR gene is important for EVERYONE at all stages of life, but...

Did you know that about 50% of the population has a mutation on one or both of their MTHFR genes? Again, this is the gene that metabolizes folate (vitamin B9) to build, protect and repair your DNA. This includes switching genes on and off. It also helps with protein metabolism, detoxification and hormone function. It's extremely important!

You get one copy of this gene from your mom and one copy from your dad. In our family, my husband and I BOTH inherited two copies of this mutation-- one from each parent. This type of mutation, or genetic SNP (single nucleotide polymorphism) as it is more accurately called, means we are both homozygous (have double mutations) for the MTHFR gene which means our son is homozygous too. We found this out by running our Ancestry and 23andMe raw data through one of the many gene analysis tools available these days. Among other things, it means our ability to convert synthetic folic acid to folate and to metabolize folate in general is highly compromised. In fact, in people who have a MTHFR polymorphism (mutation) in one or both genes (heterozygous or homozygous), synthetic folic acid can convert to homocysteine which can be very inflammatory. High homocysteine is a risk factor for cardiovascular disease, pregnancy complications, mental health disorders and certain cancers.

This also means we have compromised detoxification functions. No wonder we are both chemically sensitive and get nauseous around perfume, car exhaust, dryer sheets etc.!

Even if you don't have a copy of the MTHFR mutation (SNP), as Dr. Ben Lynch states in his book, Dirty Genes, your "clean genes" can still get "dirty" or dysfunctional from toxic exposures, poor diet, poor sleep, lack of movement, chronic illness, injury, stress etc. It's likely most of us can use some extra support for our MTHFR gene. In my opinion, foods rather than supplements are the best way to obtain micronutrients-- vitamins and minerals.

By the way, if you want to learn more about the MTHFR gene and some other key player genes that can be supported through diet and lifestyle, I HIGHLY recommend picking up the book Dirty Genes. I learned SO much!

Thankfully there are many folate-rich foods readily available to us such as: leafy greens, Brussels sprouts, broccoli, asparagus, avocado, liver, peanuts and certain beans, such as pinto and black beans. Folate from whole, unprocessed foods vs. synthetic folic acid or fortified foods (like breads and grains) is easier for our bodies to absorb. Folate-rich foods also have the necessary co-factors like vitamins, minerals and enzymes that all work together to maximize nutrient absorption.

Again, one cup of black beans provides about 64% of the daily value needed folate (vitamin B9) that supports our DNA. Pinto beans actually have more folate than black beans, but I personally don't digest them as well (more on digestion coming up). When you eat a whole food vs. taking a supplement you get ALL the nutrients along with it that help it metabolize and digest properly.

That said, I do take vitamins and supplements as an insurance policy. I use and trust Seeking Health products as they test very low in heavy metals and contaminants (and they gladly provide you with 3rd party lab tests) and they have appropriate forms of absorbable folate. I still use their Optimal Prenatal as a multivitamin which has the appropriate forms of both folate and B12 for those with the MTHFR SNP.

Thankfully our son LOVES and does well on black beans. He has Down syndrome and FPIES (a rare food allergy) so feeding him a robust, properly prepared, nutrient-dense diet is on our daily menu. Black beans are a big hit for his palate and genes!

The method below will show you how to optimize digestion and nutrient-density of this power-packed legume.

But first, let's talk about one of my favorite topics: carbs and carb cycling.

Black Bean Carb Cycling

If you have read my article, How I Use Carb Cycling to Reset My Adrenals, Stress Levels and Sleep, then you will know how and why I strategically eat starchy carbs to balance my blood sugar and hormones. To say this has been a game-changer is an understatement!

In an era of carb-o-phobia (which was preceded by a long and lingering era of fat-o-phobia), I have learned to embrace the benefits of this awesome macronutrient. Since we only have three macronutrients to choose from-- protein, carbohydrates and fat-- I find that balancing all three macros at each meal makes me feel my best.

In my carb cycling article I discuss the blood sugar roller coaster that is so disruptive to stress levels, hormones and sleep. In fact, I was so strung out on this roller coaster after the loss of two loved ones and due to depriving myself of starchy, satisfying carbohydrate-rich foods believing that a diet high in mostly protein and fat was the key to health for me.

When I stumbled upon Dr. Alan Christianson's book, The Adrenal Reset Diet: Strategically Cycle Carbs and Proteins to Lose Weight, Balance Hormones, and Move from Stressed to Thriving, I learned how to use starchy carbs to balance my out-of-control blood sugar and therefore hormones.

Starchy carbs and/or resistant starches are slow burning carbohydrates that do not spike blood sugar quickly like processed white-flour carbs do-- crackers, breads, pastas, donuts, cereal, pancakes, waffles, cookies etc. When fiber-rich, resistant starches (sweet potatoes/yams, potatoes, beans, hummus, sourdough bread, certain fruits, cashews, peanuts etc.) are paired with ample protein and healthy fats, it slows down digestion which helps slow down blood sugar metabolism.

This slow release of glucose into the bloodstream helps regulate cortisol-- a stress hormone, which in turn helps regulate overall hormone metabolism, stress responses and sleep. Again, my post goes into all the details of how I use carb cycling to support my adrenal glands and my body's stress response.

Black beans were one of the easiest foods to start carb-cycling.

The Adrenal Reset carb-cycling framework includes all three macronutrients at each meal-- protein, fat and carbs. Each meal includes a palm-sized protein portion, a golf ball sized portion of healthy fat, and increasing portions of starchy carbs at each meal (plus all you can eat low-starch veggies and low-glycemic fruit) with the largest portion of starchy carbs at dinnertime to help manage blood sugar and therefore cortisol levels during sleep.

Here is an example of how I use black beans according the Adrenal Reset Diet protocol:

  • Breakfast: 2 eggs any style (1 palm-sized protein portion), 1/4 cup sliced avocado (1 golf ball sized healthy fat), 1/4 cup black beans (1 golf ball sized starchy carb), salsa (all you can eat veggies/fruits)

  • Lunch: 4-5 oz. salmon filet (1 palm-sized protein portion), 1/2 cup black beans (2 golf ball sized starchy carbs), raw cheddar cheese (1 golf ball sized healthy fat), cilantro, chopped red onion and lime (all you can eat veggies/fruits)

  • Dinner: 4-5 oz. grass-fed steak or beef (1 palm-sized protein portion), 3/4-1 cup of black beans (3-4 golf ball sized starchy carbs), taco salad: cilantro and romaine lettuce with tomato, red onion, avocado, cheddar cheese, olive oil + lime dressing (1+ golf ball sized healthy fat + all you can eat veggies/fruits)

I still use carb cycling daily and I play with the portions according to how I feel each day. You can see in my dinner example that I eat more than the recommended amount of 1 golf ball sized portion of healthy fat and a tad more starchy carbs. I try to eat according to my appetite and interest and not by exact formulas, but I definitely use carb cycling as a framework for macronutrient balancing. Again, I feel my best with all three macros-- protein, carbs and healthy fats-- at each meal. The portions of each vary with my needs, cravings and activities each day.

So with all these benefits lined up, it seems like black beans may need to get on your weekly menu. Not so fast!

Beans are notoriously hard to digest. Let's find out why and what you can do about it so you can enjoy the benefits of this magical legume.

Beans & Digestive Problems

Beans are so easy to eat, but, for many of us, soooo hard to digest! Why must this be???

First off, this convenient and delicious food is not only loaded with fiber, starch and nutrients, but also has complex sugars that are hard on our digestion. In fact, these sugars, known as oligosaccharides, can't be broken down by our intestinal enzymes like most foods can.

Instead these sugars, found in beans and other foods like wheat and some veggies (such as garlic and artichokes), cruise on down to our large intestines where they become a tasty treat for our intestinal bacteria. Yum! And that's where the gas begins.

The gas, bloating and discomfort "down there" is a byproduct of fermentation in our guts. This may not be a problem for some people since gut bacteria ARE part of a healthy microbiome -- the happy community of microorganisms living inside and outside our bodies. In fact, our good gut bacteria do a lot to support our immune system, a healthy metabolism and even our brain function.

But when we are out of balance in our digestion and in healthy vs. unhealthy gut bacteria (a.k.a. dysbiosis), the already hard-to-digest beans can set us over the edge leading to the uncomfortable bloating, room-clearing farts and sudden trips to the bathroom.

Also, the high fiber content in beans can be another challenge for our digestion. That's why proper preparation and mindful eating of beans is going to be key for your maximum enjoyment of this ancient and healthy food.

Anti-Nutrients: Phytates and Lectins

Before we get on with the proper bean preparation process, let's address the another challenge to bean digestion: anti-nutrients.

Say what??? You may or may not have heard the buzzword "anti-nutrient" floating around the health food galaxy. These are elements of plants and animals that help them defend against predators, support nutrient uptake and more.

For example, the anti-nutrient known as oxalate found in your spinach and Swiss chard acts as a natural repellent against grazing animals as well as a providing calcium regulation for the plant. How nice!

Phytates or phytic acid, found in nuts and seeds as well as beans, help these plants store the mineral phosphorous. These "anti-nutrients" are needed for plant health and survival.

The trouble comes when these anti-nutrients interfere with human gut activity and mineral absorption. Phytates, with their high phosphorous content, are thought to disrupt our absorption of other key minerals like iron, zinc and calcium.

Additionally, there is another class of anti-nutrients found in beans capable of inducing gut chaos: LECTINS!

Studies have shown that lectins can also disrupt the proper absorption of key minerals like calcium, zinc, iron and phosphorous -- think: massive nutrient robbery! Not only this, lectins can also bind to parts of our intestinal tracts wreaking havoc with nutrient absorption and gut bacteria. There is good reason we don't eat beans raw (and can't), but the way you cook them is critical to deactivating some of these gut busting anti-nutrients and gaining some serious benefits.

5 Tips for Better Bean Digestion

These 5 tips will not only address how to reduce the phytic acid and lectin content of your frijoles, but also make those tough gas-inducing sugars easier to digest.

  1. Do a 24-Hour salt brine soak before cooking. This is what greatly reduces the phytic acid and lectin content of your beans. Again, foods high in phytic acid and lectins can block absorption of key nutrients like iron, zinc and calcium which can potentially contribute to nutrient deficiencies. This step is so worth it-- especially if you are serving beans to growing kiddos. Details in recipe below.

  2. Cook beans in an Instant Pot or pressure cooker. This locks in all the nutrients.

  3. Eat beans in rotation. If you have trouble digesting beans (as seen through bloating, gas, GI issues), eat servings every few days. As soon as your GI issues subside, try again. I also find it helpful to eat beans away from other high sulfur foods like cruciferous veggies (especially broccoli, cauliflower, cabbage), eggs, cooked garlic and onions which can also be a cause of bloating and gas. Instead of eliminating healthy foods from my menu, I find eating in rotation (rather than eating a certain food at every meal, or day after day) to be a simple trick that allows me to digest and enjoy a variety of foods. This may not be necessary for everyone, but can help some.

  4. Eat beans with fresh herbs (like cilantro, epazote or parsley) or spices (ginger, turmeric, cinnamon or mint-- think side dishes) to support digestion.

  5. Take a digestive enzyme with alpha-galactosidase which breaks down the complex carbohydrates in beans into simpler sugars making them easier to digest. I like Veganzymes by Global Healing Center. The capsules include alpha-galactosidase plus a wide variety of enzymes to digest everything you can think of including animal protein. I currently use this milder enzyme called Plant Enzyme Digestive Formula by Designs for Health which contains alpha-galactosidase and a broad spectrum of enzymes including ones to digest animal protein. They both work well.

Best Instant Pot Black Beans (24-Hour Brine Soak)

Prep: 24 hours Cook: 4-1/2 hours Total: 28-1/2 hours Servings: Lots!

This recipe is SIMPLE, but takes some prep and planning due to a long soaking time and long cooking time. This is what makes the beans nutrient-dense and easier to digest! I know there is debate about soaking beans if you are going to pressure cook them. As a person who has struggled with digestive issues my whole life, I can say that I have tried ALL sorts of methods and this is the process I use for optimal digestion (along with my 5 tips above). Soaking reduces the phytic acid and lectins that can disrupt nutrient absorption. It also breaks down tough to digest sugars that cause bloating and gas. To make the effort worth it I make a big batch (using 2 pounds of dried beans) and freeze some. The best part is that this method makes some seriously creamy and delicious black beans!

The links below are affiliate links chosen for product quality and purity.


  • 2 pounds of organic black beans (I like organic turtle beans)

  • 1/4 cup of organic olive oil

  • 2-4 tablespoons of sea salt; I like Jacobsen's or Colima Sea Salt for my brine and cooking as its hand-harvested and tests very low in heavy metals and microplastics (pricey, but worth it)

  • 1-3 gallons filtered water

Instructions to Clean and Soak Black Beans:

Note: This is 24-hour soak. I try to start soaking the beans the day ahead to get a full 24-hour soak. You can also do an overnight soak of 8+ hours if you are short on time.

  1. Sort first: Spread dried beans out on a kitchen towel and remove by hand any small rocks, dirt, straw or defective looking beans (half beans are okay). A nice fine motor activity for the kiddos!

  2. Rinse or skip: If your beans are dusty or dirty (meaning they are probably fresh and authentic) rinse them well in a colander. I like this mesh colander for all my soaking projects as nothing escapes through the holes. If they are clean and shiny you can skip this step.

  3. Soak in salt brine: Place your clean/sorted beans in a large glass bowl. Put one tablespoon of sea salt on top of the beans. Cover with filtered water (I use our filtered sink water for this step) about 3-4 inches above the beans as they will expand. Stir to mix in the salt. Cover with a plate and let sit out on countertop. I like using glass for soaking beans because I don't have to worry about any acid reacting with stainless steel. I'm not sure if this matters, but it's my preference as there are a lot of colorful plant compounds leeching out in the soaking process. I use this large, lead-free Pyrex clear glass bowl for all my big soaking projects. I don't use vintage Pyrex anymore due to lead concerns.

  4. Rinse and repeat: At the midpoint in your 24-hour soak, rinse the beans in your colander, refresh the water, and repeat this last step with the salt. However, if you forget or are too tired, lazy or spaced out, they will still come out fine. I speak from experience:).

  5. Final rinse: This part is very important to minimize those lectins, phytic acid and gas-producing sugars. Rinse VERY WELL after 24 hours and put all the soaked beans in your Instant Pot or pressure cooker. Your beans are ready to roll.

Instructions to Pressure Cook Black Beans in Instant Pot:

  1. Once your well-soaked, clean beans are in the Instant Pot, fill with filtered water 2-3 inches above the beans. More water = creamier beans, so add according to your preference. I find that 2 pounds of soaked beans in my 6-quart Instant Pot means I am filling water up to the "max fill" line. It works out perfectly!

  2. Add 1/4+ cup of olive oil or avocado oil. I'm not kidding here. I learned this from my mom -- the best bean maker in the universe -- and it makes your beans crazy creamy. Try it. See how you like it.

  3. Set your Instant Pot to pressure cook for 4 hours. Yep, 4 hours. I see most Instant Pot black bean recipes pressure cooking black beans anywhere from 30 minutes to 1.5 hours. I find less time than 4 hours still leaves me with tough bean skins that are hard to digest. I only do this with black beans. You can certainly experiment with timing, but this is what I do for optimal bean digestion with a creamy texture and mineral-rich flavor. If you are in a hurry, I suggest a no less than 1.5 hours of pressure cooking.

  4. Allow for a natural, slow release.

  5. Set Instant Pot to saute for 10-15 minutes.

  6. Stir in 1 (or more) teaspoon of high quality sea salt and let simmer for 10-15 minutes, stirring occasionally. Turn off and continue to season to taste.

  7. Enjoy some hot beans with your meal of choice. They go great in this Mexican Chicken Soup with Key Lime Calabacitas or this 7-Ingredient Superfood Salsa.

  8. Once cool (which may take a while), store and freeze some in glass jars leaving about 2 inches of air between the beans and lid to allow for expansion.

What about you? Do you soak your beans or have a bean cooking method you like? Have an enzyme or trick for enjoying beans? Let me know in the comments below! I'd love to hear from you!

You can also tag me @nourishandcherish.ntp if you want to share any bean photos!


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  2. Azevedo L;Gomes JC;Stringheta PC;Gontijo AM;Padovani CR;Ribeiro LR;Salvadori DM;. (n.d.). Black Bean (phaseolus vulgaris L.) as a protective agent against DNA damage in mice. Retrieved from

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  4. Bazzano L.A., Thompson, A.M., Tees, M.T., Nguyen C.H., Winham, D.M. (2011). Non-soy Legume Consumption Lowers Cholesterol Levels: A Meta-Analysis of Randomized Controlled Trials. Retrieved from

  5. Buettner, D., & Skemp, S. (2016, July 7). Blue Zones: Lessons From the World's Longest Lived. Retrieved from

  6. St. Michael's Hospital. (2016). Eating beans, peas, chickpeas or lentils may help lose weight and keep it off. Retrieved from

  7. Hair, M., & Sharpe, J. (2014). Fast Facts About the Human Microbiome. The Center for Ecogenetics and Environmental Health, University of Washington. Retrieved from:

  8. Ilton, E. (2019). What Are Oligosaccharides? Learn All About the "O" in FODMAP! Retrieved from

  9. Jenkins, D.J., Kendall, C.W., Augustin, L., Mitchell, S., Sahye-Pudaruth, S., Blanco Mejia, S., Chiavaroli, L., Mirrahimi, A., Ireland, C., Bashyam, B., Vidgen,E., de Souza, R.J., Sievenpiper, J.L., Coveney, J., Leiter, L.A., Josse, R.G. (2012). Effect of Legumes as Part of a Low Glycemic Index Diet on Glycemic Control and Cardiovascular Risk Factors in Type 2 Diabetes Mellitus: A Randomized Controlled Trial. Retrieved from

  10. Kieffer, D., Martin, J. R., Adams, H.S., (2016). Impact of Dietary Fibers on Nutrient Management and Detoxification Organs: Gut, Liver, and Kidneys. Retrieved from

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  12. Levy, J. (2022, May 04). How to support methylation + why it's important for your health. Retrieved from

  13. López-Cortez, S., Rosales-Martínez, P., Sofía, Arellano-Cárdenas, & Cornejo-Mazón, M. (2016). Antioxidants Properties and Effect of Processing Methods on Bioactive Compounds of Legumes. Retrieved from

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  17. Winham, D. M., & Hutchins, A. M. (2011, November 21). Perceptions of flatulence from bean consumption among adults in 3 feeding studies. Retrieved from


About the Author

Roxie Daggett is a Nutritional Therapy Practitioner (NTP) with a virtual holistic nutrition practice in Sedona, Arizona. Her passions include studying nutritional research pertaining to brain health, gut health, genetics and longevity. When she is not geeking out on nutrition she enjoys cooking, hiking, organic gardening and hanging out with her wonderful husband, and her adorable, energetic son who happens to have Down syndrome. Learn more on her About page and stay in touch by grabbing your FREE BRAIN HEALTH BREAKFAST GUIDE above or below!


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