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How to Make a Healing Protocol for Your Autoimmune Disease Treatment

Anna Disease Management & Treatment, Living Well with Autoimmune Disease 6 Comments

This is Part 2 of our Autoimmune Healing Protocol series.  The first part of this series is:

Why You Need a Healing Protocol for Your Autoimmune Disease

laptop and notebooks with text overlay - Autoimmune Disease Treatment: How to Make an Autoimmune Healing Protocol (& Why You Need One)Do you know that it IS possible to minimize autoimmune disease symptoms, reduce antibodies, and even completely reverse your disease using all-natural methods?

It is.  I am a living example.  I have a whole mess of autoimmune antibodies and symptoms!  But barely feel a thing as long as I’m on top of living my autoimmune-friendly life.

Here’s the thing though…

It’s not easy.

I wish I could tell you that it was.  I wish I could be like some of those people who are like “Budgets made simple!”  Or… “Don’t have time to cook?  Here are thirty-five 10-minute nourishing meals!”

But, “Autoimmune disease made simple” isn’t really a thing.  There are just so many moving parts… so many root causes and interventions.  What’s even worse is that you could literally follow everything I’ve done to the T and make zero progress because your root causes are different than mine.

There is good news though.  There are ways to make it easier.  Like A LOT easier.  I’m talking years shaved off your healing journey.

The answer to your prayers, and how to cut down your healing process is to create a personalized Autoimmune Healing Protocol.  Yes, it’s a mouthful, and if you’ve never heard of it or you’re not convinced it’s for you, be sure to read this post.

But, of course, before you jump right into a healing protocol… you have to actually make one!

So, in this post, I am going to summarize how I personally go about creating my healing protocols.  I’ve made many, and they are so, so, SO helpful.

**Please remember – this is not medical advice!  I am not a doctor and I’m not trying to be one.  The best companion for making your own healing protocol is a highly-knowledgeable, well-qualified medical practitioner who listens to you and is willing to work WITH you on your healing journey.

5 Steps to Making a Healing Protocol for Your Autoimmune Disease Treatment

Step 1: Learn about your disease.

I’ll just come right out and say it – many, many doctors (not all) offer lackluster care when it comes to autoimmune disease treatment.

If you don’t believe me, or my personal experience (or my husband’s), then join any autoimmune disease Facebook group and see the frustration among the members with their doctors either ignoring them, telling them their crazy, or just offering drug after drug after drug with horrendous side effects.

My point?  Your doctor might be able to offer some helpful experience and testing, but if they fall short elsewhere, then there are plenty of other options for building your autoimmune expertise.  Thankfully, you have some awesome resources that will make the job easier for you.

One of the most important steps to any and all healing is to educate yourself and become your own advocate.  If you’re ready to learn more than the majority of people you’ll ever meet, then your first stop is The Autoimmune Solution by Dr. Amy Myers MD or Beat Autoimmune by Palmer Kippola.  

Both books are relatively short, and to the point!  You can breathe a sigh of relief, because I know how overwhelming all of the information can be.  In our opinion, there is no better place to start.  Our only advice is to just pick one at the beginning and then move on to other resources when you are ready.

(For a complete list of resources, check out our List of the Best Autoimmune Resources in our free member’s only toolkit.  Click here to gain access.)

Like anything important, learning requires you to take time and focus-in so you can digest the information.  Take notes.  Re-read if you have to.

Now that you have the knowledge, you are one step closer to beginning your protocol.  The best benefit of a healing protocol is that it helps you USE the information that you spent so much time absorbing.

Step 2: Start looking for your root cause – gather opinions, test results, and other data.

Initial consultations with your doctor (or team of doctors) will provide you with: their opinion and suggested tests, which may or may not be helpful.  You’ll also have the information from reading a book like Beat Autoimmune which points you towards less conventional topics like:

  • Diet
  • Gut Health
  • Nutritional deficiencies
  • Specific infections that are commonly associated with autoimmune disease
  • Mold and toxins
  • Liver function
  • Emotional and physical trauma (do not underestimate this one)
  • Much more.

And as you learn about all of this, you might think to yourself “Hmmm, the symptoms of magnesium deficiency sound a lot like me.”  And you’ll write that down in your health journal so you keep your thoughts organized.

Or… maybe you know for a fact that you have some sort of irritable bowel syndrome going on after you eat specific foods.  So, you might be thinking you have some food sensitivities.

And, if you’re like the majority of people, you’ll realize that your diet is filled to the brim with inflammatory foods, and you likely have leaky gut.

BAM!  See what’s happening here?  You are connecting your unique symptoms, signs, and lifestyle choices to possible root causes. 

From there, you can do two things:


  • Wait on ordering those tests.  Here’s why:

I’ve worked with two types of doctors – some who want to do all the testing upfront and others who just want to do some basic testing for things like nutritional deficiencies. 

I have one doctor, for example, who believes that there is no need to test for infections of any kind, because if you address nutritional deficiencies and clean up your diet, your body will have the right tools to fight off infections on its own.  On one hand, I agree, but, there are some downfalls to this thinking, which is why I also have another doctor on my team who likes data and testing. 

So, use your best discretion here… sometimes, it isn’t necessary to test and treat for all root causes at the beginning if a diet or lifestyle change can give your body the ability to clear it.  It might be more useful (and cost effective) to wait until you really feel like you’re stuck and are no longer making progress.

Step 3: Learn about interventions based on findings from Step 1 and 2.

Okay, so Step 1 gives you the clues to look for on your journey.  Step 2 uses test results, or your educated gut feeling about possible root causes to point you in the direction of areas you need to address.

Now, Step 3 you’re going to research interventions.

What’s an intervention?  It’s what you’ll be doing for treatment/healing.  So, a healing diet like the Wahls Protocol, for example, is an intervention.  Or using herbal remedies to eliminate parasites is another example.   Prescription drugs are one too.

There are so many possibilities, y’all.  This is where things go haywire though.  You’re not always going to nail the right intervention for every step of your healing journey.  The successes AND failures are part of the process.  Embrace it.  There is real benefit from the knowledge you gain with each failure, and even more when something works.

My biggest advice?  Pick the interventions that make the most sense to you (with the guidance from a trusted functional medicine doctor).  And keep moving.

Now let’s talk about how to plan your implementation.

Step 4: Divide the intervention(s) into small actionable steps.

Now that you have your list of interventions, it’s time to breathe.  If your list looks like this… you might be overwhelmed:

  • Strict Autoimmune Paleo Diet for 60 days before reintroducing foods
  • Gut healing foods and supplementation to repair leaky gut damage and rebuild lining
  • Switching to non-toxic cosmetic products to reduce inflammatory toxins
  • Taking supplements to address nutritional deficiencies

Remember when I said this isn’t easy?  This is what I’m talking about!

All of a sudden, the life you used to know could be completely turned upside down, flipped inside out, and you’re thinking… “There’s no way I can do this.  I’m too busy.  I want to eat whatever I want.  I don’t have the money.  This will take up too much time.  I don’t enjoy cooking.  I won’t ever remember to take all these supplements.”

Yes, I’ve visited every one of those excuses.  Multiple times.  I get it.  But then I realized this is my health.

Autoimmune disease is a cry for help.  And if you listen to your body and tend to its needs, you can live a healthier, fuller life.

So now it’s time to take that list and divide it into smaller, actionable steps.  Let’s make a plan, so it doesn’t feel so overwhelming anymore.

For example… committing to a strict Autoimmune Paleo Diet for 60 days might look something like this:

  1. Read our post on how to start and stick to an autoimmune healing diet.
  2. Pick your start and end date.
  3. Buy or rent Autoimmune Paleo cookbooks.
  4. Using the recipes and tips in the cookbooks, make a meal plan.
  5. Using the meal plan, make your shopping lists for each week (some books even include these meal plans and shopping lists so the work is done for you!)
  6. Clear your schedule to allow time for extra cooking and meal prep.  Maybe invest in an Instant Pot to make things easier.
  7. Etc.

Use this step to prep for what’s about to go down.  How will these interventions fit into your life?  What will your roadblocks be?

Grab a friend for support, or join an autoimmune disease support group.  This is hard, but you are never alone.  People are doing it all day, every day, and they are after the same goal as you… they just want to feel better.

My one word of advice – don’t get stuck here.  Okay, that’s 4 words.  But you get it.  Some of us are planners.  We love to plan!  But then we plan… and plan… and continue planning.  For months, even years.

Move on to Step 5 ASAP to avoid this common obstacle.

Step 5: Execute.

You’ve made it.  Hopefully by now, you have a well-thought-out healing protocol, full of small actionable steps and you are SO READY to get this show on the road.


This is the fun part.  If it’s the right protocol for your body and root causes, you should start feeling better soon.  Like real soon.

If it’s not quite the right direction, then remember, you checked it off the list and you’re ready to find something else that will work.  There will be something that works.  I promise.

A health journal is a great companion for this step because it tracks your progress and connects you to your body’s signs and symptoms as you move through your protocol.  Otherwise, you might miss some pivotal observations, or… if you’re on the right track, you might even forget how sick you were (which is well-needed encouragement, sometimes)!

A Healing Protocol is one of the Best Tools for BEATING Your Autoimmune Disease

Looking down the barrel of an autoimmune disease is scary.  Trying to figure out how to overcome it and put it into remission is… scarier.

But taking the time to develop your own healing protocol makes the whole process seem manageable, doable, and possibly even… dare I say it, FUN.  By creating a plan to learn about your autoimmune disease, root cause the trigger(s), decide the methods to overcome it, and finally execute, you give yourself a fighting chance to heal.

The trouble is, without a healing protocol, you are left wandering your path without a real guide.  A doctor can be a great help, but they don’t always have all the answers.  Developing your own protocol with input from your doctor, your own research, and input from friends gives you a much better chance of success.

And when things do become overwhelming, you will have already broken down your steps into small actionable chunks to reduce or eliminate the stress.  The result – you can keep chugging along and winning the war against your disease.  Even just the teeny-tiniest baby steps every day can add up to more than you think.

It’s time to get organized and take control!  You can do this.  Just follow the steps:

  1. Learn about your disease.
  2. Look for your root causes.  Gather doctors’ opinions, test results, and other data.
  3. Learn about interventions based on Step 2.  Pick which ones you want to use.
  4. Plan your intervention implementation.
  5. Execute your plan!  Keep a health journal along the way.

And, remember to give yourself a little grace… this might be new, and a lot of information to absorb, but there’s nothing better than victory when it comes to reclaiming your health.

Do you have a personalized healing protocol?  If you feel like sharing, please tell us what you’re trying and what’s working for you by leaving a comment below!

laptop and notebooks with text overlay - Autoimmune Disease Treatment: How to Make an Autoimmune Healing Protocol (& Why You Need One)

Comments 6

  1. I was very interested to read your thoughts on autoimmune protocol.

    I have MS and was diagnosed in 1994. Quite early on my MS journey, I became aware of the powerful effects of a paleo diet.

    My source of information is Dr Terry Wahls and her Wahls Protocol. I started following this dietary regime and was astounded by the results.

    I have tried various interventions, over the years, but, the Wahls Protocol has been the only one with measurable, positive results.

    I suspect that a leaky gut was the trigger or root cause of my condition but, this requires further investigation..

    1. Post

      Hi Stephen, I share my personal experience using the Autoimmune Protocol in this post. I found it a really useful tool for identifying my food sensitivities, some of which stuck around (walnuts, eggs, dairy, grains) and others that eventually went away as I continued to heal my gut. Interesting what you say though because after all of my reintroductions using the Autoimmune Protocol, I’ve landed on a diet very, very similar to the Wahl’s Protocol (a few minor tweaks) and it has also given me measurable, positive results. I have a post on how I landed on that diet coming soon, but I am not surprised to hear that you’ve had great results. I think her major emphasis on low sugar and high vegetable intake is key, and I’ve noticed those two components aren’t as highly emphasized on other healing diets. Glad you found something that works, Stephen!

  2. I have 4 autoimmune disorders. I’m feeling overwhelmed about trying to keep up with all I need to do or avoid etc. Do you have any suggestions on how to keep it all straight? I currently have a folder but think a journal would be more manageable, but there are some things that overlap 2 or more of them and some that apply to only one. How do I keep it all straight?

    1. Post

      Hi Linda, I can definitely relate to how overwhelming it all feels. I’ve personally benefited from a health journal in this situation, but something that has really helped me is to approach all my autoimmune conditions as one, rather than separate conditions, because they are all related to dysfunction of the immune system which needs to be modulated in order to reverse them. A book like The Autoimmune Solution, Beat Autoimmune, The Wahls Protocol, or Goodbye Autoimmune Disease might help you keep things straight, because those books focus on a single approach to treat a variety of autoimmune conditions.

  3. Great advice! I started taking control of my own protocol back in 2014. That was the year I almost died because my physicians didn’t take me or my symptoms seriously. Laying in the hospital was my wake up call- only I was responsible for my health and life. It’s not easy, far from it. Many physicians will ridicule a patient for knowing too much about their conditions. But, WE live with the conditions 24/7. Who better than the patient to know what is going on?

    1. Post

      Hi Rosanna, you are exactly right, and good for you for taking charge of your health! That is ultimately what this comes down to… like you said, WE are the ones living with this, and we are the ones who can put a stop to it. Thanks for reading. 🙂

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