Food sensitivities and immune tolerance: looking beyond food

Food sensitivities are becoming increasingly common, yet many people still think that the solution is simply to remove trigger foods and to avoid them long-term. While removing certain foods can temporarily reduce symptoms, it doesn't always explain why sensitivities develop in the first place.

For many people, food sensitivities are linked to something called immune tolerance [1].  This is the immune system's ability to recognise what is safe and what is harmful. When immune tolerance is working well, the body can respond to infections and threats while staying calm when exposed to food proteins, beneficial gut bacteria and the body's own tissues.

When immune tolerance becomes reduced, the immune system can become more reactive. This can show up as food sensitivities, but also sometimes as skin issues, fatigue, digestive symptoms or sensitivity to chemicals and smells. This change usually happens gradually rather than suddenly and is often linked to overall stress on the body rather than one specific food. 

Why food reactions can worsen over time

Many people notice they start reacting to one food, and then over time they seem to react to more foods. This an feel frustrating and confusing. 

The immune system does not see foods the way we do. It looks at tiny protein patterns within foods (I always liken this to a barcode). If two foods have similar protein structures, the immune system may react to both. This is sometimes called cross-reactivity.

This becomes more likely when the immune system is already under pressure, especially if digestion is poor or the gut lining is irritated. Over time, repeated immune activation can make the immune system more sensitive.

The gut plays a major role in food tolerance

A large part of the immune system sits in the digestive tract. The gut lining acts like a filter. It allows nutrients into the bloodstream while keeping the largest particles, bacteria and toxins out.

When digestion is working well and the gut linking is strong, the immune system is exposed to fewer potential triggers. When digestion is poor or the gut lining becomes more permeable, the immune system is exposed to more food particles and inflammatory signals. 

The gut microbiome – the bacteria living in the digestive tract – also plays a major role [2]. Beneficial bacteria help train the immune system to respond calmly. When microbiome diversity is reduced, immune reactivity often increases.

Why immune tolerance can break down

Immune tolerance is influenced by many health factors, not just diet. Often, several pressures happen at the same time.

Some common contributors include:

• ongoing stress
• poor sleep
• digestive problems
• diets low in fibre or plant-based foods
• nutrient deficiencies [3]
• high exposure to environmental chemicals
• multiple courses of antibiotics throughout your life
• ongoing inflammation

Why the goal is often immune balance, not immune boosting

Many people assume they need to "boost" their immune system. However, with food sensitivities, the immune system is often already overactive. The goal is usually to help it become more balanced and less reactive.

Supporting immune balance often includes:

• eating a varied, fibre-rich diet
• supporting gut health
• supporting sleep and stress regulation
• supporting nutrient status, such as omega-3 fats and vitamin D
• supporting blood sugar balance

These steps help the immune system respond appropriately rather than overreacting.

Where supplements may help

Supplements can sometimes support immune tolerance, but they usually work best alongside diet and lifestyle changes rather than replacing them.

Supplements are often most helpful when supporting specific systems, such as:

• immune balance
• gut lining repair
• microbiome support
• detoxification support
• stress and nervous system regulation

Taking a large number of supplements isn't always better. Often targeted support works best.

Where food sensitivity testing fits in

Food sensitivity testing can sometimes be helpful, but it is often misunderstood. Testing is not usually designed to give a permanent list of foods to avoid forever. Instead, it can help identify patterns and guide short-term dietary decisions.

Testing may be helpful if:

• symptoms are unclear
• multiple foods seem to trigger symptoms
• a structured reintroduction plan is needed

However, results should always be interpreted alongside symptoms and health history.  Some people show reactions to many foods on testing, which can sometimes reflect immune stress rather than true long-term intolerance. 

Why long-term food restriction is not always helpful

Removing foods can reduce symptoms in the short-term. However, long-term restriction can reduce gut bacteria diversity and make tolerance harder to rebuild. In many cases, the long-term goal is to slowly and safely increase food variety while supporting immune and gut health.

A whole-body approach to improving your enjoyment of food 

Improving food tolerance usually involves supporting several systems at the same time.  This may include:

• supporting digestion
• supporting gut lining health
• increasing dietary diversity gradually
• supporting stress and sleep
• supporting detoxification
• reintroducing foods carefully and slowly

This approach focuses on helping the immune system feel safe again, rather than simply avoiding foods long term.

Food sensitivities often reflect a wider change in immune tolerance rather than a permanent problem with specific foods. Supporting gut health, immune balance, microbiome diversity and overall health can help improve food tolerance over time.

Food sensitivity testing can sometimes help guide decisions, but the long-term goal is usually rebuilding tolerance and expanding safe food choices wherever possible. For many people, this means moving away from fear of food and towards a more flexible, confident relationship with food. 

References

1. Satitsuksanoa P, Jansen K, Głobińska A, van de Veen W, Akdis M. Regulatory Immune Mechanisms in Tolerance to Food Allergy. Front Immunol. 2018 Dec 12;9:2939. doi: 10.3389/fimmu.2018.02939. PMID: 30619299; PMCID: PMC6299021.
2. Almansour N, Al-Rashed F, Choudhry K, Alqaderi H, Sindhu S, Al-Mulla F, Ahmad R. Gut microbiota: a promising new target in immune tolerance. Front Immunol. 2025 Sep 18;16:1607388. doi: 10.3389/fimmu.2025.1607388. PMID: 41050659; PMCID: PMC12488628.
3. Huang M, Shao H, Wang Z, Chen H, Li X. Specific and nonspecific nutritional interventions enhance the development of oral tolerance in food allergy. Crit Rev Food Sci Nutr. 2024;64(28):10303-10318. doi: 10.1080/10408398.2023.2222803. Epub 2023 Jun 14. PMID: 37313721.