7 Unexpected Foods That Can Cause Digestive Issues

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.

This is Part II of the Elimination Diet series. Read Part I.

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.

We are all different, with different digestive systems, microbiome compositions, and food intolerances. For each one of us, the foods we eat will either feed digestive problems or feed a healthy gut. The problem is knowing which foods do which things for you. Food intolerances are highly individual, but over the years in my practice, I have seen some common food culprits that tend to be to blame, and that, when eliminated, often solve many digestive issues that seemed intractable. Here are the likely offenders:


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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.

In addition to this, many people with gut issues can be sensitive to casein, even in organic milk. Casein is the main milk protein and a common irritant. If you have digestive problems, try removing dairy for a while to let your digestive system heal. See if it makes a difference for you. Fermented dairy, such as grass-fed kefir and yogurt, is usually better tolerated and also offers beneficial bacteria for the microbiome, but some people can't tolerate dairy in any form.

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. Don't think artificial sweeteners are the answer, though - research shows that they also decrease the good bacteria in the gut, which could also cause glucose intolerance and lead to diabetes.

6. Nuts and seeds

The roughage of nuts and seeds can be difficult for some people to digest. On top of that, most nuts sold in stores are coated in inflammatory industrial seed oils, like soybean or canola oil. 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 can allow your gut to heal. Then you can slowly reintroduce nuts and seeds to see if they're an issue for you are not. We are all different. Some people can handle them every day; some can only handle them in small amounts.


This funny sounding acronym stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. In other words: fermentable sugars. These short-chain sugars are not fully digested in your gut and can be excessively fermented by your gut bacteria.

This fermentation releases hydrogen gas that could lead to distension of the intestines - which can cause major IBS symptoms in some people like pain, gas, bloating, constipation, and diarrhea. Most of the high-FODMAP foods are actually healthy, real foods. But even when it comes to natural foods, what works for one person may not be right for everyone.

Here are the foods that should be avoided or severely limited if you have IBS symptoms, to most effectively work toward healing your gut:


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

To really find out what foods your body can - and can't - handle, I recommend trying out an elimination diet. I'll walk you through the steps to healing your gut and uncovering food intolerances in my mindbodygreen course.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. 

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

Gut Feelings Dr. Will Cole 6

Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel