Regulate the Immune System Before Going After Pathogens

When you are living with autoimmune disease, mould-related illness such as Chronic Inflammatory Response Syndrome (CIRS), or any chronic inflammatory condition, it is tempting to go straight into “killing protocols” — targeting Candida, parasites, Lyme disease, or viruses like Epstein–Barr. But from a functional medicine perspective, this is rarely the right first step. Before attempting to kill pathogens, we must first focus on regulating and rebalancing the immune system. Otherwise, aggressive treatment can overwhelm the body, worsen inflammation, and trigger severe flares.

Perhaps you have a diagnosis like Hashimoto’s thyroiditis, rheumatoid arthritis, or psoriasis — or maybe you have symptoms that strongly suggest immune dysregulation but no formal diagnosis yet. The internet is full of advice, supplements, and “quick fixes,” and many of our clients arrive feeling completely overwhelmed by conflicting information and unsure which step to take first.

This blog is entirely about laying the groundwork — putting everything in place to help your immune system work as it should, before you consider antimicrobial or antiviral treatment. Once your immune system is supported and balanced, you may even find that you no longer need a killing protocol because your body is finally able to handle its pathogen load naturally.

Why You Should Regulate Before You Kill

Chronic illness is rarely caused by a single infection. More often, it is the result of a perfect storm of nutrient deficiencies, gut dysbiosis, mould or toxin exposures, chronic stress, poor sleep, and immune dysregulation. If you skip over these factors and go straight to antimicrobials, you risk worsening symptoms rather than getting better. A dysregulated immune system may overreact, causing excessive inflammation, or underreact, leaving you unable to clear pathogens effectively.

The first step is to put your immune system in the best possible position to do its job — regulating inflammation, managing infections, and protecting you without overreacting.

Building a Strong Foundation: Step by Step

Step 1: Test, Don’t Guess

We often begin with key blood tests to evaluate vitamin D status, iron stores, inflammatory markers, and other important nutrients. For example:

• Vitamin D: Essential for regulating immune function. Low levels are linked to increased autoimmunity and worse outcomes in conditions like Hashimoto’s and rheumatoid arthritis. Test your levels rather than guessing — and aim for the optimal, not just “acceptable” range.

• Iron: Iron is a cofactor for many immune processes. Both deficiency and overload can impair immune function. Ferritin, serum iron, and transferrin saturation should be checked before supplementing.

• Omega-3 to Omega-6 Balance: Chronic inflammation is often worsened by an imbalance between pro-inflammatory omega-6 fats and anti-inflammatory omega-3 fats. A simple blood test can help guide whether supplementation with fish oil or algae oil is needed.

These are the building blocks your immune system needs to work properly. Without them, you risk staying stuck in a state of chronic inflammation, no matter what killing protocol you try.

Step 2: Protein Intake and Nutrient Absorption

Protein is essential for producing immune cells, antibodies, and enzymes. Most people with chronic illness do not eat enough high-quality protein. We calculate your needs and help you meet them through food or supplements if necessary. We also investigate whether you are absorbing the nutrients you eat — for example, low stomach acid or gut infections can prevent proper digestion and absorption, leaving your immune system under-fuelled.

Step 3: Optimising Gut Health

A healthy gut is key to a balanced immune system. If your gut is inflamed or imbalanced, your immune system will be too.Around 70% of the immune system resides in the gut-associated lymphoid tissue. If you suffer from "IBS" such as bloating, diarrhoea, constipation, reflux, or alternating bowel habits, you may not be breaking down and absorbing nutrients well. Stool and SIBO testing can uncover dysbiosis, overgrowths, and markers of inflammation that need to be addressed before more advanced protocols.

Step 4: Sleep — Your Nightly Reset Button

Quality sleep is one of the most powerful immune regulators available. Poor sleep keeps your immune system in a state of high alert and drives inflammation. If you wake frequently, struggle to fall asleep, or wake unrefreshed, we work with you to identify why — whether due to cortisol imbalances, blood sugar drops, a histamine dump, or environmental factors — and correct them. You need restorative sleep before your body can safely handle the stress of targeted antimicrobial treatment..

Step 5: Addressing Stress and Trauma

A constantly activated stress response keeps the immune system overactive and reactive. Functional medicine looks at your coping mechanisms, daily stress levels, and past trauma that may be keeping your nervous system in fight-or-flight mode. We may suggest nervous system regulation tools, counselling, or even adaptogenic herbs that are safe for your condition. Lowering stress is not optional — it is essential for regulating immune function.

Step 6: Personalised Nutrition and Immune Modulation

A carefully planned, short-term elimination diet can remove major immune triggers and give your system a rest. This is not about permanent restriction but about creating a low-inflammatory environment so that the immune system can reset and regain balance before you consider any pathogen-focused treatments.

The Goal: Regulate First, Target Later

Once these foundations are in place — nutrients are optimised, gut health is supported, sleep and stress are improving — your immune system is in a much better position to manage its own pathogen load. At this point, we can reassess: do we still need to target Candida, Lyme disease, or viral reactivation, or is the immune system now coping on its own?

Many clients find that once the immune system is supported, symptoms like fatigue, pain, and recurrent infections reduce dramatically without aggressive “killing” protocols. For those who still need targeted antimicrobial or antiviral therapies, these treatments are far more effective and better tolerated when the groundwork has been laid.

From Overwhelm to Empowerment

This process can feel like a lot to take in — but you do not have to do it alone. Working one-on-one with a functional medicine practitioner gives you a clear plan, an additional set of eyes on your case, and guidance on what to prioritise first.

Our job is to help you break the process into manageable steps, making sure you build a strong foundation for lasting change.

When you get this right, the results can be truly life-changing: improved energy, fewer flares, better mood, improved gut health, and greater resilience. This is the work we love to do at The Autoimmune Clinic — guiding clients with Hashimoto’s, rheumatoid arthritis, CIRS, and other complex chronic conditions back toward balance and vitality.

Muriel Wallace-Scott, Functional Medicine Practitioner

At The Autoimmune Clinic, we support clients step by step, guiding them through what we feel is most needed to strengthen their immune system and overall health.

If you would like to explore working with us, please do not hesitate to email us at hello@autoimmunecliniclondon.com or BOOK A DISCOVERY CALL with one of our practitioners to discuss how we can help you on your journey back to wellness.