Food Intolerance Elimination Diet – Do It Properly

Elimination Diet

An estimated 20% of today’s population suffer from food intolerances and allergies, and this is set to continue rising in the years to come. At present, there are no known cures for these conditions. However, an elimination diet can improve a person’s tolerance to certain foods and is the gold standard for identifying and improving food intolerance reactions. It is used as a therapeutic measure, alongside addressing factors such as digestive and immune health, to both improve a person’s quality of life and avoid any long-term food restrictions that could be damaging to nutrient status and long-term health.


This article is going to cover the reasons why we might use an elimination diet, what tolerance is and how it can be developed, and what is involved in the various stages of an elimination diet including the ongoing maintenance phase. This type of diet should always be done with a doctor or naturopath to ensure your safety and to avoid any nutritional deficiencies that may develop.

Elimination diet basics.

In a nutshell, an elimination diet is one that removes particular foods from your diet. These foods are either foods that are known to cause you issues or foods that your practitioner recommends you remove due to your specific symptoms. For example, you may need to remove high FODMAP foods, or high histamine foods etc. If you react to many things and aren’t sure where the issue lies, then the most beneficial approach is to remove a wide range of foods (which are reintroduced later). 

Alternative you can take our hair intolerance test, which will give you a list of foods that your body reacts to. You can use this list as the basis of your elimination diet. This stage of removing foods lasts up to 4 weeks, or until all symptoms are gone. The foods are then reintroduced, one at a time and any reactions carefully recorded. This process can take up to 6 weeks, or longer if your case is complex.

Is an elimination diet necessary?

Yes, an elimination diet is often a necessary part of managing food intolerances for the long term. It also helps to identify any foods that you may not be aware are causing you issues.

It is common these days for people to feel ordinary all the time. We can experience low energy, frequent headaches, brain fog, poor memory and concentration, aches and pains and more every day; and we often may not realise that the cause of this is found in our food. In fact, food intolerances can cause such a wide array of symptoms that it would be easy to miss their relationship to what is on your plate. These symptoms can include:

  • Alternating constipation and diarrhoea
  • SIBO and bacterial imbalance in the gut
  • Reduced food breakdown and low stomach acid or enzymes
  • Nutritional deficiencies such as iron or Vit D
  • Exhaustion or general tiredness
  • Systemic inflammation
  • Detoxification issues, headaches and migraines
  • Skin rashes
Every body-system can be impacted, and performing an elimination diet is an excellent first approach in identifying and treating food intolerances.

Tolerance Explained

The human body has three main defence mechanisms or barriers that block entry into the body. They are the skin, the digestive system and the respiratory system. When foreign matter enters these channels, each individual reacts in differing ways. This reaction can be undetectable, or it can go as far as being a severe allergic reaction. Our reaction to specific substances or foods is called our tolerance level.

The factors below have been identified as having a direct effect on our tolerance levels.

Our immune system – specifically how well it functions. If it is not strong, this can significantly affect our tolerance to substances. Cells called ‘mast cells’ in our immune system can degrade in response to foreign matter, and release histamine in vast quantities. This is what gives rise to allergic reactions, heat swelling etc. The immune system and mast cells can be supported to remain stable through things like Vitamin C and herbal tonics.


Our digestive system – the gut lining is of particular importance here. If it is damaged and leaky gut has occurred, then the body can react quite quickly to any foods that are eaten. Food particles get through the gut lining and into the bloodstream, giving rise to both immune and digestive reactions.


Microbial balance in the gut – if this balance is not correct, then the overproduction of harmful bacteria can cause inflammation, gas, diarrhoea, constipation and other digestive reactions when specific foods are eaten.


The mechanical function of the stomach – this includes stomach acid and enzyme production. If these things are not efficient, then food can’t be broken down properly. This causes digestive issues and inflammation along the gastrointestinal tract.

It’s important to understand these factors because they could be the basis of your food intolerances. Your practitioner will work with you to strengthen these area’s of your health during your food intolerance treatment.

Finding your tolerance level.

Undertaking an elimination diet is the way to find out what your tolerance level is. After you’ve removed the foods, you take careful note of how your body reacts when you consume that food again, and at what quantity. For example, you may be able to have a serving of the food twice a week with no reaction, but if you have it a third time you react. Twice a week is your tolerance level to that food. This tolerance level can change over time, especially if you work on healing your gut and immune system. You can retest at any time to see if your tolerance level has increased.

Elimination diet steps.

There are three main steps to a proper elimination diet:

1 – Rest. This is the food elimination stage of the diet.

2 – Reset. This is when your practitioner will give you individualised herbal and nutritional medicines to restore your digestive and immune health. This ideally aids you in tolerating more foods.

3 – Challenge. This is the stage where foods are reintroduced into your diet, one at a time. Any reactions are carefully recorded, along with the quantity and frequency of eating the food.

Stage 1 – Rest

This initial stage of an elimination diet is designed to allow your digestive system to rest from the inflammatory effects of eating foods you are intolerant too. This improves the integrity of your digestive system and dampens any immune reactivity at the same time.

Your practitioner will select the foods that are removed in this stage based on your specific symptom picture. There are lists available on the internet that recommend what foods to remove, but we recommend you do this under the guidance of a healthcare professional.

This stage is only meant to be short term, and the foods you remove here will not need to be removed forever.

Foods are then reintroduced into your diet after all your symptoms are gone. The process of symptom elimination can take up to 4 weeks. If you still have symptoms after this time, they may be unrelated to food intolerances. Investigating this further with a health care provider is recommended.


Stage 2 – Reset

This stage is designed to improve your digestive function, immunity and overall health. Nutritional and herbal medicines are strategically prescribed to heal your body, which will ideally increase your ability to tolerate particular foods in stage 3.

To achieve the best healing in this stage, work with a Naturopath/Nutritionist who is experienced in this area.

Stage 3 – Challenge

The challenge phase comes after rest and reset, specifically when your symptoms are resolved. Here we outline a basic approach for reintroducing foods:

Introduce only one food at a time, for one day only. Then take two rest days back on the elimination diet. IF you do not react to the food during this period, then try consuming it for two days in a row, with one day off after that. If you find that you do not react, then it is generally regarded as safe to include that food in your diet moderately. 

Eating it twice a week is considered a moderate amount. Make sure that you carefully track the food you are eating and your symptoms during this phase, including things like changes in your sleep and mood, as well as any digestive issues. This will allow you to find your tolerance level, and also find any foods that cause you problems.

Depending on the number of foods that were eliminated, and the severity of symptoms. You may need a long term maintenance stage.

The maintenance stage

This stage is critical if your diet is still quite restricted because any long term restriction of whole food groups or large amounts of foods creates a potential risk of nutritional deficiencies and resulting issues. This is extremely important in children, but also concerning for adults too. This stage must also be undertaken with a qualified practitioner to avoid any health problems arising.

During this phase, everything learnt from Stages 1 to 3 of the basic elimination diet will be used by your practitioner to design a maintenance program for you. Foods that still trigger you will be strategically reintroduced, with the aim of allowing you to consume a wide array of foods within your tolerance limits.

There are three steps for each trigger food, and they are as follows:

Step 1:

Consume the trigger food for one day out of 7. Make sure there are at least five days in between. Eat this food once a week for four weeks straight. If you react during this time, have a two-week break from the food before recommencing another four week period. If you can tolerate eating this food once a week for four weeks straight, continue on to step 2.

Step 2:

This step is the same as step 1, but you consume your trigger food for two days out of 7. Maintain this for four weeks straight. If you react during this time, then have a two-week break before recommencing another four week period of eating the food twice a week. Continue onto step 3 when you can tolerate eating this food for four weeks straight at a rate of twice a week. 

Step 3:

This is also the same as step 1, but you consume your trigger food now for three days out of 7. When you can tolerate eating this for four weeks straight, at a rate of three times weekly, then you can maintain this long term. However if you can only tolerate it at a rate of twice weekly, this is ok too. Twice weekly is your tolerance level, the amount at which your body can handle without any reaction.

Completing this maintenance phase can be time-consuming, but it is also rewarding and allows for nutrient diversity within your diet.

As a great support on your elimination diet journey, our bio-resonance hair intolerance test will give you a list of your trigger foods. You can then use this as the basis for your elimination diet ‘foods to remove’ list. Really take the guesswork out of it. Purchase your test HERE today.


An Elimination diet is the current gold standard in healing from food intolerances. It is a step by step approach which eliminates specific reactive foods from a persons diet, and then strategically reintroduces them one at a time in order to either increase tolerance to that food or identify the person’s tolerance level. Tolerance levels are the amount of a specific food that a person can have without any reaction occurring. 

This article covers the main steps of an elimination diet and how to do them. The steps are:

1# Rest. This is where the food is eliminated from the diet completely, allowing the body to rest and recover from any inflammation and reactions caused by the food.

2# Reset – This is the healing phase, where your naturopath or nutritionist will use specific supplements to help your digestive tract recover.

3# Challenge – this is the stage where the foods eliminated in phase 1 are strategically retested.

After these three phases, you enter what is called the maintenance phase. It is designed to help those who did not reach conclusive answers in the challenge phase above. It allows the most diverse diet possible within a person’s limits. 

Finding your long term tolerance levels will allow you to live a life free from food intolerance symptoms, but still filled with nutrient diversity.

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