Still Having Digestive Problems While Eating Paleo

Melissa McEwen of wrote an awesome post about why people eating Paleo, Primal, low-carb, GAPS, or some similar diet might have stomach problems, even if they never had them before they started the diet. I strongly recommend you check out that post if you haven’t totally resolved your digestive issues on this kind of diet, or if you suddenly started having indigestion, bloating, diarrhea, constipation, stomach cramps, or worse. She briefly goes over some possibilities for your toilet troubles, including the following.

  • Powerful “cleanses” can irritate your gut.
  • Increasing your intake of FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols), which are in everything from nectarines to cauliflower, can irritate your gut.
  • A lot of foods–even Paleo or Primal foods–have toxins in them. If you overeat them, you might not feel so great.
  • Fermented foods like kim-chi and sauerkraut aren’t always great for everyone, especially not in large quantities.
  • High fat diets can take some time to get used to, and so can high protein diets.
  • Certain supplements, or taking a ton at one time, can irritate your gut.
  • Sometimes people don’t eat enough, which can cause gas, bloating, constipation, etc.
  • Some people with gut issues just have an underlying, covert food poisoning or parasite situation going on and should be tested and treated for it by a medical professional.
  • Some people have something bigger happening, like Crohn’s or ulcerative colitis, or even major thyroid issues, and diet alone may not be able to fix it. Those people need to be treated by a medical professional.

I’m just going to put in my two cents on digestive issues because I think it’s a common problem. For instance, my good friend has been Paleo to a tee for years and struggles with bloating, cramping, and constipation. She just recently decided to make some of the changes discussed in this post to her diet and she’s having some success. There are things you can consider and actions you can take to figure out what’s going on.

Food Sensitivities and Intolerances
Like Melissa said, all foods can be toxic. Once you’ve wrecked your gut, just because you go Paleo or get on a “clean” diet doesn’t mean you’re instantly healed. You might still be developing food sensitivities to things that are perfectly legal on these diets because your gut is still wrecked. It can take years, or a lifetime to heal it. Eggs, nuts, coffee, tomatoes, and coconut products (especially coconut milk because of the guar gum and FODMAPs) are very common culprits. Experiment with removing those things from your diet one at a time for a couple weeks each to see if they’re causing problems for you.

If you take all those things out and you’re still having problems, you’ll want to start digging a little deeper. Maybe you never really ate beef before and now you’re eating it with two meals a day, but you’ve actually had a sensitivity to it all along. There are tests you can take (I do the LEAP food sensitivities test) to figure that out.

Some foods are just hard to digest. For instance, there’s been a smattering of gaseous, raucous noises in our household since we started eating tart-skinned plums. I stopped eating them when I realized the detrimental effect and all is fine with me. Unfortunately, my husband has refused to stop eating them…

Digestive Supplements
In the beginning, a lot of people don’t have enough stomach acid or enzymes to digest the hearty foods they’re now eating, especially the extra meat. It’s ok – that can be remedied. Protein is digested in part by hydrochloric acid (HCl) in your stomach. A lot of people don’t produce enough HCl when they first start eating Paleo because their bodies aren’t accustomed to all that protein. When you supplement with HCl and digestive enzymes for a while, your body often starts creating enough of those things on its own again. Without HCl and enzymes, your food just rots in your digestive system, causing bloating, heartburn, diarrhea, constipation, or gas. Here’s a blog post about how to supplement with HCl properly. Do not supplement HCl if you are on medication for heartburn or if you have a known ulcer.

As for enzymes, go to your holistic health practitioner, health food store, natural pharmacy, or online and buy a high quality enzyme spectrum supplement. It’ll be an inexpensive capsule containing enzymes that help digest carbs (amylase), protein (protease), and fat (lipase). Take the recommended dose at each meal with your first bite for a couple of weeks to see if that helps.

Remember that in the first month of changing your diet, anything can happen. You might have diarrhea, cramping… you might even throw up because you’re detoxifying. Give it some time and your issues will likely abate.

Being stressed can cause a lot of problems with digestion, so if you’re going through some big life event, not getting enough sleep or exercise, or you’re just generally anxious, work on that and see if it helps your gut. You know the ways: therapy, taking more time for yourself, yoga, meditation, sex, painting, whatever works for you. I know someone who had diarrhea for literally a year straight and when she broke up with her boyfriend and moved out of her house, it went away. Guess it was a stressful relationship…

Get Help
If you do all those things and you still have problems, you may want to get checked out by a naturopath. They can run digestive tests on you to see what kinds of bugs might be living in your gut – parasites, yeast, bacteria, etc. They can help you get rid of those things. Don’t be afraid to admit that you can’t do it all on your own!


Anyone else have anything to add?






    1. Linda Howell – LEAP is a blood test that checks for the amount of immune mediators that are activated when your blood comes into contact with each of a long list of foods. They check 120 foods and 30 food additives/chemicals. They tell you how sensitive you are to certain foods and then you remove those foods for as long as it takes to heal your gut and get rid of your symptoms. I’ve seen people have success with it and I’ve seen others not have success with it. It’s $395 through me. You can email me at if you have any other questions or want to do the test.

  1. Kefir, kefir and more kefir!!! I have struggled with food allergies, severe digestive issues, toxic mold, thyroid and adrenal issues for three years now. (I eat Paleo, but still had troubles). My whole life was so compromised…. I started with goats milk kefir, made at home of course, but have switched to water kefir.
    I cannot begin to tell you the difference in my life, and how much better I feel.
    It took about three months for the full effect and positive changes. I drink a glass in the morning, and again at night before bed. I am so thankful my daughter got us started on it!

  2. When you eat a high fiber diet, you need to make sure you are drinking enough water. Otherwise you can get very bad intestinal cramps.

  3. I am a Naturopathic Doctor practicing in Colorado and Utah. Ive found that the majority of people feel great eating paleo. For those that do not there are several digestive enzymes and functional tests to check for adverse food reactions(a combo of food allergies, food intolerance and food sensitivities). Once these are identified through IGA, IGG and IGE blood tests, most people reap the benefits of paleo while individualizing the diet to their specific needs. I lost weight, have decreased pain and inflammation in my body and work with others especially those with autoimmune disease.

  4. I’ve been on paleo for about 9 days and have been feeling great besides the diarrhea. I’m really struggling with bad stomach pains, churning and explosive runs to the bathroom. I tried to get rid of nuts but it’s still happening. Any ideas?

    1. Lindsay – Hmmm… Your body may just still be adjusting to the change. It’s possible you aren’t producing the enzymes you need to digest your food properly. I’d get a digestive enzyme spectrum from a health food store and take the recommended dose with every meal and large snack. Do that for 2 weeks and see if you feel any better.

  5. I’ve been doing paleo since just before Christmas. I’ve had huge stomach problems also, frequent trips to the bathroom, bad mucus, diarrhea, cramping, irritability, lethargy . I’ve tried eliminating foods like coconut, cauliflower and other FODMAP foods, chia seeds, I’ve tried introducing probiotics and i’m still struggling. I was expecting stomach problems for a week or so while my body adjusted to the changes, but I was hoping after a month I’d be feeling the positive effects people keep talking about. Any more suggestions to make this easier, so I’m more likely to stick to it? Thanks :-)

    1. Kristy – That sounds awful. Are these symptoms worse than before you were Paleo? Is there any other food you added in bulk to your diet? If you’re eating a lot of nuts and seeds, I’d remove those and see how you feel. It might be that. Or you may have an egg allergy and now that you’re eating a lot more eggs it’s showing up full force?

  6. I had some symptoms before I was paleo, and they were undiagnosed, even after a series of tests (cameras, bloods, stool), but they are alot more frequent, and onset quicker than before. I’m not a huge egg fan, so i’m not eating many of those. I’ll give the seeds and nuts a miss and see how that helps. I don’t want to give this up yet, I know it’ll take some serious tweeking to work, but i’m reaching my wits end to work out what to eliminate. Thanks again.

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