Reset your Gut with an Elimination Diet

An elimination diet is a powerful tool in understanding your chronic illness or symptoms. Functional Medicine stresses the importance of a food first approach to health. Diet forms the foundation of lasting health. Truly, many symptoms can be alleviated or disappear entirely based on lifestyle factors, and chief among these lifestyle factors is the food you eat. Changes in diet can have widespread effects, not just on the digestive system. It’s common for food to be a root cause of joint pain, brain fog, mood swings and more. This occurs because of food intolerances, allergies, and inflammation in the gut. The best part of the elimination diet is that it’s free. If you decide to undergo this process, with proper planning you could be feeling better in a few weeks at no greater cost to you.

Why an elimination diet?

An elimination diet removes foods from your diet that may be at the root cause of your health problems. It resets your gut health, which in turn affects the health of your other body systems. The state of your gut is connected to hormonal health including the adrenals and female hormones.

It resets your relationship with food. In the beginning, it may be more difficult to go without those sweet or fried foods, but at the end you may find a new appreciation for carrots, zucchini, broccoli, etc. This gets us back to our roots (sometimes literally). Our ancestors, and their bodies, knew these natural whole foods well.


An elimination diet also teaches us which foods cause adverse reactions. At the end, you will reintroduce foods back into your diet one at a time. This reveals problem foods for your particular constitution. I remember after doing my first elimination diet, I ate a snack bar with a high amount of sugar. I hadn’t had that amount of sugar in over four weeks. Within minutes I was having heart palpitations and difficulty with mental concentration. Before the diet, my body had acclimated to this level of sugar, but after removing it from the foods I eat, my more finely tuned body was having an obvious response.

What’s wrong with problem foods?

Problem foods contain antigens that alert the immune system, causing an inflammatory reaction in the gut. This leads to the destruction of gut tissue, which in turn causes problems with the absorption of important nutrients and minerals. With the gut tissue destroyed, it also leaves the body vulnerable to the passive absorption of toxins into the body. If this is a problem, those processed foods filled with chemicals may overload your detox pathways.


Problem foods also alter the gut microbiome, causing dysbiosis. The microbiome is the garden of your body. It needs a balance of healthy bacteria and viruses to operate optimally. This community of microbes are responsible for many processes, including supporting the immune system and amino acid production. Some estimates say that up to 95% of the body’s serotonin is made in the gut. Guess what is an important part of the serotonin production process. That’s right, healthy bacteria are important for the creation of all this serotonin. If the community of bacteria are unbalanced from the diet, this could be one cause of decreased serotonin production, leading to mood disorders such as depression.

What is the Elimination Diet?

On the elimination diet, you will be removing the most common problem foods for 4 – 6 weeks. This is not a calorie restrictive diet. You may eat as much of these foods as you want. Although the purpose of this diet is not to lose weight, some people do find they do drop some pounds.

What foods do I eliminate?

  • Acohol
  • Beef
  • Chocolate
  • Coffee, soft drins, energy drinks, tea
  • Corn
  • Dairy products
  • Eggs
  • Gluten-containing grains (barley, rye, spelt, and wheat)
  • Peanuts
  • Pork
  • Processed meats
  • Shellfish
  • Soy and soy products
  • Sugar (white sugar, high-fructose corn syrup, brown sugar, sucrose, etc.)

What Food Can I Eat?

  • Dairy alternatives
  • Fish
  • Fruits
  • Game meats
  • Gluten-free whole grains (amaranth, bucwheat, millet, quinoa, rice, teff, etc.)
  • Healthy oils
  • Legumes (except soy and peanuts)
  • Nuts (except peanuts)
  • Poultry
  • Seeds
  • Vegetables

How to implement

I would advise against jumping in without first doing some preparation. Take a couple of weeks to familiarize yourself with what you can eat. On your trips to the grocery store, start reading the labels on packages. Don’t be surprised if you can’t eat most foods you find. It’s more about focusing on the healthy fruits, vegetables, meats, and nuts/seeds that you can have.

Create a plan for what you’ll eat during the day. Think of the most difficult times during your day when it’s easy to just grab what’s available. How can you prepare in advance for meals you’ll need during your workday or on a trip? Choose the foods you would like to eat and recipes you would like to prepare.

Do not skip meals. Intermittent fasting is helpful in many cases, but this is not the time to implement it. Eat plenty of the foods in the righthand column of the table above and eat throughout the day.

A Word of Caution

This diet can dramatically shift the microbiome in the gut. Unhealthy levels of bacteria or parasites may decrease. This means that these problem microbes will die in large amounts, releasing the toxins they produce into the gut. This is called a Herxheimer reaction. It means that there may be a temporary increase of toxins released in the beginning weeks of the diet, and your symptoms may worsen before they get better. I advise that you seek the guidance of a medical professional before starting this diet.

Reintroducing food

To get the most out of the diet, it’s important to reintroduce the foods you have eliminated in a systematic way. Choose one food at a time to reintroduce. In one day eat two big servings of that type of food. Then wait three days to see the effects that is has on your body. Waiting three days is important, because some types of foods can have delayed reactions (i.e. gluten). If that food is a problem, keep it out of your diet for now, and retest it after you have reintroduced all the other types of foods. However, if there is no reaction with a type of food, you know that it is not a problem for you, and you may include it in your everyday diet. If you have had a problem with anaphylaxis and allergic reactions to foods, please use caution when reintroducing foods. Seek guidance from your healthcare professional.

Eating Disorders

This diet may not be appropriate for people with eating disorders.

Social Support

An elimination diet may be a daunting endeavor for those eating the standard American diet. Lifestyle changes like this work better if a group of people decide to do it together. Check with your family members or friends to see if they would be interested in resetting their gut health. Together, you will be stronger.

If you need additional support to meet your health goals, I am available for online consultations. You can sign up for my free 15-minute consultation below.

Disclaimer: This website does not provide medical advice. The information contained on this website is for informational purposes only. No material on this site is intended to be a substitute for medical advice, diagnosis, or treatment. Always seek the advice of a healthcare professional with any questions you may have regarding a medical condition and treatment before undertaking a new healthcare regimen.