How Food Processing & Leaky Gut Can Impact Your Immune System leading to an Autoimmune Condition

Did you know? The way we prepare food - cooking, baking, frying, fermenting, barbecuing - can change its proteins in ways your immune system might not recognize. When combined with a compromised gut barrier (“leaky gut”), this can trigger chronic symptoms or even autoimmunity.

What Is Leaky Gut?

Your gut lining is designed to let nutrients into the bloodstream and keep larger, potentially harmful substances out. But due to stress, infections, toxins, antibiotics, or ultra-processed foods, this lining can become permeable (“leaky”). When that happens:

Partially digested food proteins can slip into the bloodstream, where your immune system treats them as foreign. When your immune system does not recognise something it mounts an attack, often by creating antibodies.

At the root of sleep disturbances are often hidden stressors, including:

• Hormonal imbalances (especially cortisol and DHEA)

• Blood sugar dysregulation

• Chronic stress (mental, emotional, physical, and chemical)

• Liver detoxification issues (especially if you wake between 1–3 a.m.)

• Inflammation and gut dysfunction

• Nutrient deficiencies and food sensitivities
  

Why This Matters with Processed Foods:

• Cooking and processing create “neo-antigens” - new protein structures that are harder to digest.

• These altered proteins are more likely to escape into the bloodstream through a leaky gut.

• Once there, they may trigger IgG, IgA, or IgE immune responses, sometimes leading to inflammation, allergies, or even autoimmune reactions.
  

Testing Gaps: Why Standard Food Sensitivity Tests Miss This

Most labs test only raw food extracts, but most people eat food that is cooked or processed. This means that reactivity to food in its real-world form often goes undetected.

Example: A person may test negative to raw tomato - but still react to cooked tomato sauce or ketchup.

The Cross-Reactivity Risk

Some processed food proteins resemble human tissues, like:

• Myelin (brain and nerves)

• Thyroid

• Pancreas (e.g. insulin-producing cells)
  

This is called molecular mimicry and can cause the immune system to attack both the food and your own tissues - an important factor in autoimmune conditions. For example, gluten is a protein found in wheat, and one part of it - called gliadin - can cause trouble for some people, especially if they have a leaky gut. When the gut lining becomes too porous, bits of gliadin can slip into the bloodstream. Your immune system sees this as a threat and starts making antibodies to attack it. But here’s the problem: parts of gliadin look very similar to your thyroid tissue. So, in trying to protect you from gluten, your immune system may accidentally attack your thyroid too. Over time, this “mistaken identity” can lead to autoimmune thyroid conditions like Hashimoto’s.

What changes from person to person is:

• The trigger (e.g. gluten, dairy, virus, toxin, bacteria)

• The tissue it resembles (e.g. thyroid, joints, brain, nerves, skin)

So...

• If gluten resembles thyroid tissue, it may lead to Hashimoto’s.

• If a virus resembles joint tissue, it could trigger rheumatoid arthritis.

• If a food protein resembles myelin (nerve coating), it may contribute to MS.

• If a chemical or microbe mimics pancreatic beta cells, it can drive Type 1 diabetes.

  
  

A recent article, “Immune Reactivity to Raw and Processed Foods and Their Possible Contributions to Autoimmunity” by Vojdani et al. (2025), draws on over 150 scientific studies and original lab data exploring how food processing impacts immune reactivity and autoimmunity.

What the Research Found:

• Many people had stronger immune reactions to processed foods than to raw ones.

• Some processed foods share protein structures with the brain, thyroid, and gut

• Advanced glycation end-products (AGEs) which form when foods are browned or fried (like grilled meats or pastries), are compounds which are highly inflammatory and may increase the risk for autoimmunity and neurodegenerative issues like Alzheimer’s, RA, thyroid conditions and MS.

What You Can Do:

• Choose whole, minimally processed food.

• Limit ultra-processed items (ready-meals, packaged snacks, fried foods)

• Consider food testing that includes both raw and cooked forms

• Track how your body responds to foods prepared in different ways

• Work with a functional medicine practitioner to build a food plan that supports your immune health

This is exactly why my Gut & Health Reset Programme is designed not just to ease symptoms, but to help you identify your personal food and gut triggers, repair a leaky gut, and calm immune over-activation - the root drivers behind many autoimmune and chronic health issues. After months of working on this programme, it is finally ready and soon to be launched. Look out for the Early Bird discount if any of the information in this article resonates with you and you feel ready to take charge of your health.