Tips for Coping with an Autoimmune Flare Up

An autoimmune flare up is a temporary worsening and intensification of symptoms. There is usually something that triggers a flare. I would say the most common ones are a period of stress - an emotional event, a significant trauma, or a period of being overworked and/or under-rested. 

Symptoms can get severe and intense — fatigue, pain, difficulty getting out of bed, brain fog & difficulty thinking, difficulty doing daily tasks are all common.

Today I’m going to discuss what to do if you’re experiencing a flare. It can get very emotional for some people — not knowing what caused it, not know how long it will last, fear of disease progression, etc. It’s tricky because stress can lead to a flare, and a flare can cause more stress. It’s SO important to acknowledge the emotional stress while ALSO addressing what’s happening physically. More on that in a moment.

Before we get there, I want to point out that this discussion assumes that you’ve already done some digging on your own to assess the root cause of your illness.

If you haven’t, be sure to read my last post How to Test for Autoimmune Triggers & Root Cause.

This blog is the transcript from Episode 67 of the Funk’tional Nutrition Podcast. For more details & elaboration on this topic, be sure to listen to the show!

How do we balance the immune system?

The goal in addressing autoimmune disease is to restore balance to the immune system. In order to do that, you have to address immune triggers, or antigens.

So the first step is to discover triggers, then remove the antigen(s) provoking the immune attack + reduce the overall antigen load. And then from there it’s about balancing the immune system.

Support T-regulatory cells.

T reg cells: 

  • help regulate inflammation and autoimmunity

  • help to restrain the immune system and prevent an excessive response

  • stop our immune cells from attacking our own tissue

With autoimmunity, T reg cells don’t always do their job well. They can start to act erratically — they might issue too much of or not enough of an immune response.

If you’ve got autoimmunity, there’s a good chance that you’re deficient in T reg cells or that they’re dysfunctional. 

Ultimately, to manage autoimmune symptoms, we want to encourage T reg cells to do their job effectively and dampen the inflammatory response.


These particular supplements Support T-regulatory cells and therefore help to balance the immune system.

In addition to my normal daily supplements, I ramp all these up during a flare.

A note on TH1 vs TH2 dominance:

TH stand for T-helper cells — they are part of the immune system and should work together back and forth in a well balanced immune system. However, in the case of autoimmune disease, you might have dominance with one of the other.

This is important when it comes to immune-stimulating supplements because certain compounds stimulate TH1 response while dampening the TH2 response, and vice versa. You want to be sure with autoimmunity — especially during a flare — that you’re not taking immune stimulators that could potentially make your situation worse.

How to determine if you are TH1 or TH2 dominant:

(Keep in mind some people have both elevated)

  1. Cytokine panel

  2. Supplement challenge (I don’t recommend this unless under the care of a practitioner — and even then you must be careful because it can push you into a flare)

  3. Self assessment based on symptoms

TH1 pushers:

(these stimulate TH1 response and dampen TH2 response)

  • astragalus

  • echinacea

  • maitake mushroom

  • licorice

  • lemon balm

TH2 pushers:

(these stimulate TH2 response and dampen TH1 response)

  • green tea extract

  • pine bark

  • white willow bark

  • resveratrol

  • pycnogenol

Below I will outline compounds that modulate both TH1 and TH2 and are therefore have less of a chance of causing problems.

Quick note:

Clinically and personally, I use a lot of Apex Energetic supplement. They are strictly a practitioner line, so you cannot purchase online (or if you can, they’re WAY more expensive). If you are interested, you can find their products on my online dispensary here. But I’ll also include Amazon links to other brands for you.


Although glutathione can be taken as a nutritional supplement, most forms are not absorbed well and do not raise levels within the cells. (For this reason, I use Apex Trizomal Glutathione.) Other methods of delivering glutathione include IVs and nebulizer. These are effective, but can be expensive and hard to access as you must see a doctor/naturopath to have them administered.

Here are two well-absorbed forms of supplemental glutathione:

Liquid liposomal glutathione

(this has best absorption)


Another option:


(this is a glutathione precursor and is more affordable than most glutathione supplements)

Vitamins A & D

Most people with autoimmunity have low levels of vitamin D. If you have autoimmunity make sure to keep your levels in a good range — A lot of autoimmune experts what to see levels around 50 ng/mL — I’ve heard up to 80 for ideal range. Levels above 100 ng/mL may indicate a vitamin D overload.

I’m not a huge fan of just blindly supplementing with high doses of vitamin D — I think it’s important to get your serum 25-hydroxy vitamin D tested first. 

Typical doses of vitamin D for autoimmune management can range anywhere from 5000 to 10000 IU per day. Some people take higher doses, especially if they have a genetic inability to absorb it sufficiently.

I like Apex Ultra D Complex, but this is another decent product, although it does not contain vitamin A


Even though it’s a smart practice to work spices like turmeric into your cooking for diversity purposes, you cannot obtain doses high enough from foods to be therapeutic and dampen autoimmunity.

Dosage is hard to generalize because it is not based on body weight or age but instead on the degree of inflammation. You must use trial and error, starting with a standard initial dose and gradually increasing the amount until you obtain the best results.

I use Apex Turmero and I also like this one.

High dose Fish oil

Therapeutic dose of fish oil is pretty high - 3-5 grams in order to lower inflammation.

This is a clean fish oil.

Short Chain Fatty Acids

The product I use is Apex Enterovite, because it contains all the short chain fatty acids. But this is a good butyrate product.

It’s also important to eat a plant-rich diet with lots of variety in plants and fibers.

CBD Oil & Full Spectrum Hemp

CBD also has a modulating effect on T reg cells and the immune system. I alway use Coyote River Hemp because I trust them. If you have specific questions about products or dosing, reach out them at:


Probiotics can be a good bet for autoimmune issues, although you might have to be careful with TH1/TH2 dominance.

Food & Diet

When I’m experiencing a flare, it’s back to food basics:

  • Nutrient density

  • Quality protein, quality fat and veggies

  • Low sugar

  • Low antigen load (remove the biggest food triggers)

The food plans in Fueled+Fit and Carb Compatibility Project check all these boxes.

Other things to consider:

  1. Add in nutrient dense organ meats, like liver and sardines

  2. If your autoimmune disease involves gastrointestinal problems — IBD or otherwise — then you might be better off sticking with slow cooked meats and veggies, soups and stews and broths. They can be a lot more gentle on an aggravated and inflamed GI tract.

  3. 12 hour fast to allow body time and space to heal

    This MIGHT NOT be appropriate for you if you have blood sugar and/or cortisol dysregulation!!

  4. Limit caffeine

  5. No alcohol



(deep, profound rest)



“Horizontal days”

Quiet time & Mental white space

Simplify your schedule & learn how to say no

Give yourself permission to be in “healing mode”

Release the expectations others put on you

Movement to tolerance

For me, flares usually involve no exercise. I can’t push myself. When I start feeling better, I will do outdoor walks, woods walks, restorative yoga, etc.

This is not the time to try to get after your #goals

Epsom Salt Baths & Sauna Therapy

I love this detox bath recipe

Minimize exposure to environmental antigens

This includes water-damaged buildings, chemicals, plastics, fragrances, conventional body care products etc.

Consider looking into Beautycounter products to avoid more chemical antigen exposure

Increase your body’s own natural production of opioids

A great way to boost regulatory T cell activity is by increasing your body’s production of opioids by doing things that make you feel good in a positive way.

enjoyable movement

socializing with people you enjoy



sex & orgasms

healthy touch

gratitude practic

feeling love

heart space meditation 

play & fun

body work:

Wendy Durham Massage & Bodywork

Distance Reiki:

Kendalyn Banks

Caroline Woodard


There are 3 main types of stress:

  • dietary

  • inflammatory/pain

  • emotional - the biggest one

Flare ups are often an invitation for us to acknowledge and evaluate the emotional component.

I find that the longer you live with chronic illness, the more willing you are to look at this side of things. The more willing you are to ask:

Am I open to believing that illness is here to teach me something?

You need to address the physiological piece — searching for root cause, eating well, reducing antigen load, restoring balance, etc. But we also can’t ignore the emotional and energetic component.

These are the questions I ask myself during an autoimmune flare up:

What is my body telling me? What does my body need?

What is my soul telling me? What does my soul need?

If you are having a hard time accessing this side of things yourself, here are some practitioners that can help you:

Noetic Balancing & Spiritual Coaching with Jessica Flanigan

Emotional Freedom Technique/EFT with Cheri Keirsted

Tracking triggers

Last, but not least, keep track of your symptoms, flares and triggers so you can start to notice patterns.

I hope this helps some of you during a tough time! XO