7 Unexpected Foods That Can Cause Digestive Issues | Dr. Will Cole

7 Unexpected Foods That Can Cause Digestive Issues

William Cole, leading functional medicine practitioner, is an expert at identifying the underlying factors of chronic conditions and offering natural, holistic approaches to optimal health. This week, we’re thrilled to share his series on the elimination diet and how it can improve your overall well-being. To learn more, check out his new course, The Elimination Diet: A 60-Day Protocol to Uncover Food Intolerances, Heal the Gut, and Feel Amazing.

Digestive issues are a big deal. They can go far beyond temporary constipation or the occasional bloating or stomach ache. Problems like chronic stomach pain, bloating, indigestion, acid reflux, GERD, constipation, diarrhea, and IBS can wreck lives. In fact, a staggering 70 million Americans are affected by digestive diseases, incurring $141.8 billion every year in medical costs.

My job as a functional medicine practitioner is to find the root reasons why patients are experiencing health issues and GI issues are some of the most common problems people face.

1. Grains

By now, most of us are aware of the possible negative impact of gluten for some people. However, I believe that in a few years research will find a similar – and possibly even worse – harm from even gluten-free whole grains. Grains contain an abundance of amylose sugars which could cause inflammation, may unfavorably skew microbiome balance, and which contain anti-nutrients such as lectins and phytates, which bind to the intestines and can hinder nutrient absorption in the body. I recommend removing all grains for a time, during an elimination diet, and then slowly reintroducing them to see how they work for your system, or whether you are particularly sensitive to certain kinds.

2. Alcohol

Regular consumption of alcohol can potentially negatively influence almost every system in your body. For the gastrointestinal system in particular, alcohol can be a trigger for leaky gut syndrome and gut inflammation in some people.

3. Legumes

Legumes include all beans (kidney, garbanzo, black, fava, etc.), lentils, peas (dried and fresh), peanuts, and edamame and soy products (tofu, soy milk, miso). There are several reasons why legumes can cause digestive problems.

Peanuts in particular contain aflatoxin (toxins produced by a mold) and lectins, while soy also contains phytoestrogens. All of these could irritate the digestive system. While other legumes may not be as bad, I’d still recommend removing them for awhile to let your gut heal. Reactivities are highly individual and may be limited to certain legumes and not others.

4. Dairy

In most major dairy farms, cows are given hormones and antibiotics, live in unhealthy conditions, and are fed GMO corn instead of grass. Their milk is then pasteurized and homogenized and the fat, with all its beneficial fat-soluble vitamins, is removed. That’s why I consider most dairy in the U.S. to be junk food.

5. Sugar

Obvious, right? But do you know why? Sugar is the favorite food of more pathogenic gut bacteria that can cause many gastrointestinal problems, so when you eat sugar, you are feeding the bad guys so they can crowd out the good guys that do nice things for you. An imbalance of bacteria in your gut can also lead to negative effects on your body’s metabolism and immune responses, and overgrowth of bad (sugar-loving) bacteria can also cause inflammation, which can eventually lead to an autoimmune-inflammatory response.

6. Nuts and seeds

The roughage of nuts and seeds can be difficult for some people to digest. They could also contain partially hydrogenated trans-fats, which can contribute to digestive problems as well. It’s best to buy them raw and lightly toast them yourself to make them easier for your body to digest. However, if you have digestive issues, it’s best to go off of nuts and seeds for awhile to see if your symptoms improve.


This funny sounding acronym stands for Fermentable , Disaccharides, Monosaccharides and Polyols.


Artichokes, asparagus, beetroot, celery, garlic, onions, leek bulb, legumes, pulses, Savoy cabbage, sugar snap peas, sweet corn


Apples, mango, nectarines, peaches, pears, plums, watermelon


Milk, cream, custard, ice cream, soft cheeses, yogurt


Rye, wheat-containing breads, cereals, crackers, pasta


Cashews, pistachios

If you want to learn more about your own health case please check out our free health evaluation. We offer in person as well as phone and webcam consultations for people across the country and around the world.

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