7 Sneaky Foods That Could Be Causing Your Digestive Issues

Functional Medicine Practitioner By William Cole, IFMCP, DNM, D.C.
Functional Medicine Practitioner
Will Cole, IFMCP, DNM, D.C., is a leading functional medicine practitioner with a certification in natural medicine and a doctor of chiropractic degree.
7 Sneaky Foods That Could Be Causing Your Digestive Issues

William Cole, DC, a 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.

Like many things in life, digestive health is only appreciated after it's gone. Problems like 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.

Reset your gut

Sign up for our FREE ultimate gut health guide featuring healing recipes & tips.

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, microbiomes and food intolerances. But overall, the foods we eat will either feed digestive problems or feed a healthy gut.

Here are the most common food culprits that could be hurting your digestive health:


1. Grains

By now, most of us are aware of the possible negative impact of gluten. However, I believe that in a few years research will find a similar—and possibly even worse—harm from even gluten-free grains. Grains contain an abundance of amylose sugars which could cause inflammation, as well as 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.

2. Alcohol

Almost every system in your body can be negatively affected by regular consumption of alcohol. In regards to the gastrointestinal system, alcohol can be a trigger for leaky gut syndrome and gut inflammation.


3. Legumes

Legumes is a food category that encompasses all beans (kidney, garbanzo, black, fava, etc.) lentils, peanuts, edamame and soy products (tofu, miso).

Peanuts 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.

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 more sensitive to casein, the main milk protein. If you have digestive problems, dairy should be removed for awhile to let your digestive system heal. Fermented dairy, such as grass-fed kefir and yogurt is usually better tolerated and also offers beneficial bacteria for the microbiome.


5. Sugar

Sugar can actually encourage the growth of bad bacteria in a person’s gut. And an imbalance of bacteria in your gut can lead to negative effects on your body's metabolism and immune responses. Overgrowth of bad bacteria can also cause aggravation and inflammation, which can manifest into an autoimmune-inflammatory response.

This includes artificial sweeteners—they can decrease the good bacteria in the gut which could then cause glucose intolerance and lead to diabetes.

6. Nuts & Seeds

If you have digestive issues it's best to go off of nuts and seeds for a temporary period until your symptoms improve. The roughage of the nuts can irritate some people's systems, so allowing for your gut to heal, then slowly reintroducing nuts and seeds can reveal if they're an issue for you or not.

We are all different. Some people can handle them every day; some people only in small amounts. You should also keep in mind that most nuts sold in stores are typically 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.



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 while you heal 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 you 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 new mindbodygreen course.

William Cole, IFMCP, DNM, D.C.
William Cole, IFMCP, DNM, D.C.
Will Cole, IFMCP, DNM, D.C., is a leading functional medicine expert who consults people around the...
Read More
More from the author:
Uncover Hidden Food Intolerances That Wreak Havoc On Your Gut
Check out The Elimination Diet
Regain your energy, vitality and health by tapping into the power of the Elimination Diet with this practical and effective nutrition course.
View the class
William Cole, IFMCP, DNM, D.C.
William Cole, IFMCP, DNM, D.C.
Will Cole, IFMCP, DNM, D.C., is a leading functional medicine expert...
Read More

More On This Topic

More Health

Popular Stories


Latest Articles

Latest Articles

Sites We Love

Your article and new folder have been saved!