The pros and cons of elimination diets for autoimmune and inflammation

Sep 23, 2022

Your digestive system is a huge portal into your body. The system is so complex (science is just starting to scratch the intestinal surface, so to speak) and lots can go wrong or swing out of balance.

Food allergies, sensitivities, and intolerances are a huge contribution to an array of inflammatory symptoms all over your body.

Things like autoimmune issues, inflammation, and even your mood can be affected by what you eat. This is because 70% of your immune system is found in or around your gut, and the bulk of serotonin is produced in this area. In fact, there are more neurotransmitters in the gut than the spinal column! 

Hello gut-brain connection.

If you have digestive issues, persistent autoimmune or inflammatory symptoms or even stubborn weight loss or gain, you may consider trying an elimination diet. This is something I often do with clients to help them regain control over their inflammation, digestion, weight and health goals.

And they are always surprised by the results because they have a GI on speed dial, or have gone for testing only to be told, "everything is normal."

When it's not.


Should you try an elimination diet for autoimmune?


An elimination diet or nutritional therapy is one where you strategically (and temporarily) eliminate certain foods to test how your body reacts to certain foods. In fact, most nutritional cleanses are based off of an elimination protocol and almost every naturopath or FMD puts their patients on some sort of an elimination diet as a first step.

Nutrition first, even from the natural doctors.

Elimination diets can help when trying to figure out if a particular food is contributing to your symptoms – or simply give your body a break so the inflammatory fire elsewhere in the body can calm down.

You generally start out by eliminating the most common food allergens for 30 - 90 days. Then you slowly add them back one at a time and note any symptoms (better or worse).

Let’s go over the pros and cons of this approach.  


Pros of elimination diets for autoimmune and inflammation


By tuning into your body's reactions to certain foods, you can pinpoint sensitivities and intolerances that may otherwise fly under the radar. This is the main benefit. Experiencing results first-hand can be very motivating when it comes to dialling into nutrition to support autoimmune.

Elimination diets are less expensive, and in many cases more reliable, than food sensitivity testing (IgG).

It can also be very empowering to be in control of what you eat, learn about food and the compounds they contain, and to try new recipes that exclude common trigger foods (meals that may become your new favourite)!

Having an easy-to-follow plan makes things much stressful (even exciting). If you love grocery shopping, cooking from scratch or trying new recipes, you’re going to draw on all these skills and have fun in the kitchen.

Some common triggers for inflammation for those with autoimmune and even those without a diagnosis, but are still experiencing imbalances include:

  • Sugar, Sulphites, Gluten, sometimes Grains, Dairy, Corn, Eggs, Nuts/seeds, Nightshades (tomatoes, peppers, egg plant), plus processed food chemicals and oils.

I understand that is a very discouraging list. Rest assured, it's a general list. You may not need to remove all of these. Various inflammatory conditions have different triggers, so there is not one diet that fits all.


Elimination diets are also starting to gain medical attention.


The Low FODMAP diet is often recommended for IBS by gastroenterologists and family doctors alike. It's also a nutrition plan I use to gauge if someone is experiencing small intestinal bacterial overgrowth (SIBO) or other sorts of digestive reactions (as in the case of Endo).

The Autoimmune Protocol is also showing great promise for reducing autoimmune symptoms. In fact, two medical studies focusing on Hashimoto's and Crohn's saw remarkable improvement in symptoms in just 12 weeks, and a third study demonstrated how AIP was able to influence DNA at the tissue level.

Studies around Paleo has shown to improve blood sugar, cholesterol and blood pressure more so than the American Diabetes Diet, or the Mediterranean Diet.

Studies around the ITIS diet (a hybrid of Paleo, AIP and the Mediterranean Diet and one I've been using for years) is gaining traction for rheumatic conditions.

The Low Histamine diet is one allergists sometimes recommend when someone is overburdened with allergic reactions.

And the best part of all of this, as you reintroduce foods (marking what your body reacts to), you end up with a customized diet that best suits your unique biochemistry … you bond with health!


Cons of elimination diets for autoimmune and inflammation


People tend to focus on only the foods to avoid and in the process, end up underfeeding themselves during the elimination process because they're not sure what to eat. This leaves them feeling hungry, tired, frustrated and under nourished. What you ADD to your plate is equally important in reducing inflammation, which leads to more energy, less inflammation, brain fog and motivation.

People often mistake other inflammatory influences for a reaction to food. Sleep, movement, stress and bowel movements can also impact reactions. You need to take a holistic view.

During the elimination process, you may not figure out everything you're sensitive to. Sensitivities can also ebb and flow depending on your environment, stress levels, exposure to toxins, etc. That's when food sensitivity testing can be helpful ... troubleshooting.

The idea of eliminating everyday foods you love, is overwhelming and is the #1 reason why people don't even try them to begin with. 

During this process, sometimes people discover that they're intolerant to one of their favourite foods, and that is disappointing.

And you are probably going to need to prepare more meals, snacks and drinks from scratch, which is time and energy that you may already be low in. Some see this as a negative .... others see it as great rewards. It depends on your mindset and what you value in your health.


What your elimination dietary plan should consider

When you're eliminating certain foods (or parts of foods, like gluten), it can be HARD! Believe, me … I get it. You don't want to feel restricted at meal time when you already feel restricted in your body or other aspects of life. That's why a plan with certain goals and milestones help.

Your plan should ensure that the most common food allergens are eliminated for your unique situation (there are different foods for different conditions). This will give you the highest likelihood of success. Working with a professional with experience will help you focus on the right foods for you. 

You also need to commit to following the plan for 30-90 days, if not longer. This can be difficult for some people, especially if you’re a social person. That’s where the plan, Reality-Based Meal Planning and practical tips to stay the course (like meal planning, product swaps and personal accountability) come in handy.

Part of a successful elimination process includes tracking your food. If you’re not used to tracking all foods and symptoms every day, it can seem like a task. Most of my clients roll their eyes at the thought of tracking food. Yet, it is something I insist on … it is a gateway to understanding your body and marking progress. You can't help yourself and I can't help clients if you're not tracking what you're eating.

You can use a simple pen and paper or a fancy app. For instance, I have a food tracking app for my clients that they can download onto their phone and simply upload photos of what they're eating and symptoms that arise. This way,

In addition to food, I also take into consideration sleep, movement, stress and bowel movements which can also influence inflammatory symptoms ... autoimmune and inflammation are reflective of nutrition, digestive, lifestyle, nervous system and environmental imbalances in total.



Elimination diets can be a very useful tool to identify food sensitivities. They can be empowering and customized and greatly reduce inflammation in the body.

However, they can be difficult to adhere to and, sadly, you may find out that you’re sensitive to your favourite foods.

If you're curious about what elimination is best for you ... and how to make that work so you can get the quickest, fastest insights and results ... reach out and we can chat.

Confused about what food, supplement or diet is best for your body & condition? Book an introductory call with Vanessa to discover how working with a nutritional professional with a decade of experience will help you improve your weight, energy, pain and digestion.

Book A Time To Talk