When I work with clients one-to-one, one of the first things I explore is what could be triggering their immune system. And no, I’m not just talking about gluten or sugar. The truth is, there are many autoimmune triggers we don’t even realise are affecting us—especially if they’ve been quietly building up in the background for years.
Today, I want to share five common autoimmune triggers I see in my practice that can lead to symptoms like fatigue, joint pain, brain fog, skin flares, and digestive issues. More importantly, I’ll show you what you can start doing about them.
1. Food Intolerances – A Major Autoimmune Trigger
Let’s start with the one I see most often: food intolerances.
Unlike allergies (which cause immediate reactions), food intolerances are often delayed and subtle. They can trigger chronic inflammation, fatigue, skin issues, or digestive discomfort days after exposure. You may not even realise your immune system is reacting—especially if the same foods are eaten daily.
This process is strongly linked to intestinal permeability, more commonly known as leaky gut. When the gut lining is damaged, undigested food proteins can leak into the bloodstream, where they’re flagged as intruders by the immune system. Over time, this contributes to immune dysfunction and flares in autoimmune conditions.
Studies confirm that leaky gut is a key factor in the development of autoimmune diseases like type 1 diabetes, rheumatoid arthritis, and lupus [source].
What you can do:
There are two helpful options here if you suspect food is triggering your symptoms:
- Do a food intolerance test like the P88 Dietary Antigen Test. This is one of the most comprehensive food sensitivity tests available. Unlike most tests that only check IgG, the P88 also measures IgE, IgG4, and complement (C3d) reactions—giving us a much fuller picture of how your immune system is responding to 88 common foods. If you’d like to identify hidden food triggers that may be worsening your autoimmune symptoms, I recommend the Food Sensitivity P88 Test I use in my clinic.
- Try a 30-day AIP elimination diet. This structured approach removes common trigger foods, reduces inflammation, and helps you identify sensitivities by slowly reintroducing foods one by one after the initial phase. It’s not always easy—but it’s powerful when done right.
Get the full AIP Guide with meal plans & recipes
In clinic, I often use both strategies depending on the person. Either way, identifying your autoimmune food triggers can make a huge difference in how your body feels—especially if you’re stuck in a flare and don’t know where to begin.
2. Chronic Stress – The Silent Saboteur
We tend to underestimate how powerful stress is—until our body forces us to slow down.
Stress affects more than your mental state. It can reduce immune resilience, increase cortisol, thin the gut lining, and increase inflammation. For those with autoimmune conditions, these effects can directly worsen symptoms or trigger new flares.
What’s tricky is that stress doesn’t have to feel dramatic. It might be subtle: poor sleep, overcommitting, lack of boundaries, or never switching off. These small stressors chip away at your system and become one of the most underestimated autoimmune triggers I see.
What you can do:
Prioritise nervous system support. This doesn’t mean meditating for an hour a day. Think: regular sleep, eating slowly, daily nature walks, even simply turning your phone off an hour before bed. Recovery doesn’t happen when the body feels unsafe—and stress tells your body exactly that.
3. Environmental Toxins – The Hidden Load
Many people focus on diet and supplements but forget about environmental exposures that constantly stimulate the immune system.
Your liver is working hard every day to detox things like pesticides, heavy metals, BPA from plastics, and chemicals in cleaning products. But if your detox pathways are sluggish—or your exposure is too high—these toxins can build up and act as chronic irritants.
Research shows environmental toxins contribute to the development and worsening of autoimmune diseases [source].
This doesn’t mean you need to live in a bubble, but small changes add up.
What you can do:
- Use a water filter
- Ditch plastic containers and canned foods (BPA is a major culprit)
- Choose fragrance-free or natural cleaning and skincare products
- Include detox-supportive foods daily (e.g. broccoli, rocket, beetroot, coriander)
Your immune system is already busy, let’s not give it more work than necessary.
4. Hidden Infections – The Stealth Triggers
Not all infections cause obvious symptoms. Some stay dormant for years, reactivating when the immune system is weak. These “stealth” infections often go undetected but can be major autoimmune triggers behind persistent symptoms.
Common culprits include:
- Epstein-Barr Virus (EBV) – linked to Hashimoto’s and lupus
- Candida overgrowth – worsens skin issues, fatigue, and bloating
- Parasites or bacterial imbalances – disturb the gut-immune connection
Your immune system may constantly fight these infections, leading to burnout, nutrient depletion, and autoimmunity progression.
What you can do:
If your symptoms aren’t improving despite clean eating and lifestyle changes, it might be time to explore stool testing or viral panels. I use functional labs to uncover what’s hiding beneath the surface—so we can support the immune system with targeted strategies, not guesswork.
5. Overtraining or Under-Recovering
Exercise is one of the most misunderstood autoimmune triggers. We’re told to move more—and yes, movement supports lymph flow, mood, and metabolism—but too much of the wrong kind of exercise can do more harm than good.
If you push through intense workouts with poor sleep or high stress, it spikes cortisol and suppresses immune repair. You may notice delayed flares, increased fatigue, or even joint pain post-workout.
What you can do:
- Aim for low-impact movement during flares (walking, yoga, light strength)
- Build in proper recovery time
- Skip workouts if you feel inflamed, bloated, or mentally exhausted
- Track how you feel 24 hours after—not just during—a session
I always remind my clients: movement should give you energy, not steal it.
So… What Are Your Autoimmune Triggers?
The most important thing to know is that you’re not “broken.” If your symptoms aren’t improving, it likely means one or more autoimmune triggers are still active—and that’s something we can absolutely work on.
These five are some of the most common autoimmune triggers I see in clinic, but they’re not the only ones. Autoimmunity is complex, and what drives inflammation for one person might not affect another at all.
That’s why working with a qualified nutritional therapist or functional medicine health consultant can be so valuable. Together, we can explore your symptoms, test if needed, and uncover the personal root causes that are keeping you stuck.
Once we identify those triggers, everything starts to shift—and your body can finally begin to heal.
What You Can Do Next:
Start with the right food plan
Grab my AIP Starter Guide + 2-Week Meal Plan and 101 AIP Recipes to help you reduce inflammation, repair your gut, and feel more confident in your food choices.
Need help identifying your triggers?
In my 1:1 consultations, I offer food sensitivity testing (including the P88 Test), gut health assessments, and a fully personalised healing plan tailored to your lifestyle.
Click here to book a free discovery consultation and start your recovery journey with expert guidance and real answers.
