A few months ago, I was speaking to a client who had reached the point where she was frightened to eat almost anything.
When we first met, she had already removed gluten, dairy, sugar, alcohol, grains, legumes, eggs, nuts, tomatoes, spinach and most fruit. She was spending hours researching ingredients, taking her own food everywhere she went and analysing every symptom that appeared after a meal.
Despite all of this effort, she wasn’t feeling significantly better. In fact, in many ways she felt worse. Her energy was lower, her diet was becoming increasingly limited, and food had become a source of anxiety rather than nourishment.
Sadly, this isn’t unusual.
One of the biggest shifts I have noticed over the past decade is how many people with autoimmune disease arrive at my clinic convinced that the answer lies in removing more foods. They have often read that gluten is inflammatory, dairy feeds inflammation, tomatoes trigger autoimmune flares, oxalates are problematic, histamine is the root cause of everything and that healing is simply a case of identifying the next food to eliminate.
Sometimes there is truth in parts of those statements. Food absolutely matters. I have seen dietary changes transform people’s health. However, I have also learned that food reactions are often far more nuanced than social media would have us believe.
The reality is that the healthiest people I work with are rarely those eating the most restrictive diets. More often, they are the people whose bodies have become resilient enough that they no longer need to react so strongly in the first place.
Why Elimination Diets Can Help Autoimmune Disease
I experienced this myself during my own health journey. Long before I became a nutritionist, I noticed that certain foods seemed to make my symptoms worse. Removing them created a noticeable improvement. At the time, it felt empowering because it was one of the first things that gave me a sense of influence over my health.
One of the biggest changes for me was removing gluten. However, one mistake I see people make is assuming that going gluten-free means simply swapping conventional bread, pasta and biscuits for heavily processed gluten-free alternatives. In reality, some of the most nourishing gluten-free foods are the ones that don’t come in a packet at all. If you’re currently gluten-free or considering it, I recently recorded a podcast episode on my favourite gluten-free swaps that actually taste good and help you maintain variety in your diet, which you can listen to here: My Favourite Gluten-Free Swaps That Actually Taste Good.
The mistake I made, and one I see many clients make, is assuming that if removing one food helps, removing ten must be even better.
Unfortunately, biology is rarely that simple.
When Restriction Becomes Part of the Problem
One of the questions I often ask clients is this:
“How much mental energy do you spend thinking about food?”
The answer can be incredibly revealing.
For some people, food has become an almost full-time job. They spend hours researching ingredients, scrolling through forums, reading conflicting advice and worrying about reactions. They have become so focused on avoiding symptoms that they have lost sight of what health is supposed to feel like.
I remember one client who arrived with a spreadsheet detailing every food she had eaten for over a year. She could tell me exactly which foods she believed triggered headaches, bloating, fatigue and joint pain. What she couldn’t tell me was when she last enjoyed a meal without analysing it.
The irony is that excessive restriction can sometimes perpetuate the very issues people are trying to solve.
A diet that is too narrow can reduce microbial diversity. It can make it harder to meet nutrient requirements. It can create social isolation. Most importantly, it can keep the nervous system in a constant state of vigilance.
The body doesn’t separate physical stress from psychological stress as neatly as we often imagine. If every meal feels like a potential threat, that matters physiologically.
Food Reactions Are Not Always About the Food
Yet when we improve gut health, reduce microbial overgrowth, support nutrient status, improve sleep and calm the nervous system, those same foods often become far more tolerable.
The food hasn’t changed.
The body’s capacity to handle it has.
This is one of the reasons I often recommend functional stool testing in practice. If somebody suddenly finds themselves reacting to a wide range of foods, I want to understand what might be happening beneath the surface. Are there signs of microbial imbalance? Is there evidence of inflammation within the digestive tract? How well are they digesting and absorbing nutrients? Are there markers suggesting the gut barrier may be under strain?
One of the tests I use most frequently is the GI Effects Comprehensive Stool Test, which is available through the Autoimmune Nutrition Clinic. Rather than simply identifying foods to avoid, it helps us explore some of the potential reasons why food tolerance may have changed in the first place, including microbiome imbalances, digestive function, inflammation, immune activity and short-chain fatty acid production. You can learn more about the GI Effects stool test here.
I think this distinction is incredibly important because it shifts the conversation from fear to curiosity.
Instead of asking, “What else do I need to remove?” we begin asking, “Why has my tolerance changed?”
That question usually leads us much closer to the root cause.
And more often than not, the answer isn’t simply another food to eliminate. It is an opportunity to better understand what the body may be trying to communicate.
A Smarter Approach to Elimination Diets
In my clinic, I rarely view elimination diets as the destination. Instead, I see them as one possible tool within a much larger strategy.
Sometimes we use a structured elimination diet because it provides valuable information. Sometimes we remove a handful of foods because symptoms clearly suggest they are contributing to inflammation. Occasionally we use more comprehensive approaches such as the Autoimmune Protocol (AIP).
However, the goal is never to create the most restrictive diet possible.
The goal is to create the least restrictive diet that allows somebody to feel well.
That may sound like a subtle distinction, but it completely changes how we approach healing.
Alongside any dietary changes, I am usually thinking about digestion, gut barrier function, microbial balance, blood sugar regulation, mitochondrial health, nutrient status, hormones, sleep quality and nervous system resilience. These are often the factors that determine whether somebody remains reactive or begins to regain tolerance.
Because ultimately, recovery is rarely about finding the one food that caused everything.
More often, it is about creating an internal environment where the immune system no longer feels the need to react so aggressively.
The Real Goal: Resilience
One of my favourite moments as a practitioner is seeing somebody realise that food is no longer taking up so much space in their mind.
They stop checking ingredients lists three times before putting something in their trolley. They can go out for dinner without spending the entire evening wondering whether they are going to flare. They stop viewing every symptom as evidence that they’ve eaten the “wrong” thing and start trusting their body again.
For many people with autoimmune disease, that shift can feel surprisingly emotional because life becomes bigger than their food rules.
Don’t get me wrong, nutrition matters enormously. Food can absolutely be part of the problem and, equally, part of the solution. However, after working with hundreds of clients with autoimmune conditions, hair loss, gut issues and chronic fatigue, I have become increasingly convinced that the goal is not to build the perfect diet.
The goal is to build a more resilient body.
A body with a healthier gut barrier. A more diverse microbiome. A nervous system that feels safe rather than constantly on alert. Better digestion, better nutrient status, more stable blood sugar, improved sleep and an immune system that no longer feels the need to react so loudly.
Sometimes elimination diets are an important part of that journey. Sometimes they provide valuable clues. Sometimes they create enough breathing room for deeper healing to take place.
What I have found, however, is that the people who achieve the best long-term outcomes are rarely the ones asking, “What else should I remove?”
They are usually the ones asking a different question:
“What does my body need in order to become less reactive in the first place?”
That question tends to lead us towards root causes rather than restrictions, and in my experience, that is where the most meaningful healing begins.
If you’re looking for a structured place to start, you can download my free guide, The Autoimmunity Recovery Plan, where I walk through the key areas I assess in clinic, from gut health and immune regulation to nutrient deficiencies, stress, hormones and lifestyle factors. It will help you start thinking beyond symptoms and towards the underlying drivers that may be contributing to your autoimmune condition.
Frequently Asked Questions About Elimination Diets and Autoimmune Disease
What is an elimination diet?
An elimination diet is a temporary nutritional approach where certain foods are removed and then systematically reintroduced to help identify whether they may be contributing to symptoms such as digestive issues, skin problems, headaches, fatigue or autoimmune flares.
Are elimination diets helpful for autoimmune disease?
They can be. In some people, removing specific foods temporarily may reduce immune activation and inflammation. However, elimination diets work best when they are used as part of a broader strategy that addresses gut health, nutrient status, sleep, stress and other root causes.
How long should an elimination diet last?
Most elimination diets should be temporary. The aim is to gather information and reduce symptom burden whilst working on the underlying factors that may be contributing to food sensitivities. Long-term restriction without a clear reason can sometimes create additional problems.
Why do I suddenly react to foods I used to tolerate?
Food tolerance can change due to factors such as gut dysbiosis, increased intestinal permeability, chronic stress, poor sleep, infections, hormonal changes or nutrient deficiencies. This is why understanding the wider context is often more important than focusing on the food alone.
Should everyone with autoimmune disease avoid gluten?
Not necessarily. Some people experience significant improvements when removing gluten, particularly those with coeliac disease or gluten sensitivity. Others notice little difference. The decision should ideally be based on symptoms, clinical history and individual circumstances rather than blanket rules.
Can gut health affect food sensitivities?
Absolutely. The health of your gut lining, microbiome composition, digestive function and immune system all influence how your body responds to food. This is one reason why I often investigate gut health when somebody develops multiple food sensitivities.
What is the best test for food sensitivities?
There is no single perfect food sensitivity test. In my clinic, I often find that understanding gut health through comprehensive stool testing, alongside a detailed clinical history and symptom review, provides more useful information than simply generating a longer list of foods to avoid.
VJ Hamilton, BSc, RNT
VJ Hamilton is a Registered Nutritionist (BANT) and an expert in autoimmune disease. VJ combines her knowledge from her medical science degree in Biochemistry & Immunology with Nutritional Therapy to offer a thorough and personalised approach to support her clients based on the most current scientific research. VJ runs a virtual and in-person nutritional therapy and functional medicine practice, The Autoimmunity Nutritionist, specialising in gut skin and immune health.