The Role of Medication on the Autoimmune Protocol

Medication and AIP

Many autoimmune diseases are marked by high levels of constant pain or severe symptoms, making it almost impossible to function without medication. The Autoimmune Protocol and conventional medicine are NOT mutually exclusive and can actually compliment each other very well. In this post, I want to talk about medication and AIP and how you can use this information to make empowered decisions in your healing. 

I was diagnosed with Ulcerative Colitis in 2013, and I have ALWAYS needed medication in order to manage my symptoms. Going without medication was never an option for me. So, it is possible to successfully implement the Autoimmune Protocol while still using medication. In fact, my experience is a perfect example of how combining AIP with medical interventions can result in higher success than just using one alone.

When Benefit Outweighs Risk

In my opinion, healing from active Autoimmune Disease is all about quality of life. Autoimmunity is a chronic condition, meaning it can never fully go away or be cured. So when we can’t “cure” our disease, the next measure of “success” is to look at our quality of life.

How do I want to feel day in and day out? Am I enjoying my life now? What do I wish were different? What do I want my life to look like?

These are all good questions to start asking yourself. Sometimes medication can offer a higher quality of life that outweighs the potential risks of said medication.

I have always been on medication for my UC. I started on lower-tier anti-inflammatories because I was afraid of the potential risks associated with stronger immune suppressing medications. As the years went by, my quality of life continued to suffer. The emotional & physical stress of my symptoms led to Diagnosis Related Depression and disordered eating.

In 2019 my desire for a better quality of life outweighed my fear and I finally decided to switch to immune suppressing medications. It was one of the best decisions I have ever made for my health. My gut was able to see enough healing so I could finally digest the nutrient-dense foods I was eating, I immediately gained weight (I had always been chronically underweight), I was able to start reintroducing more foods, I could travel again, but most importantly, my symptoms were no longer occupying 100% of my mind.

Together, AIP and medication allowed me to reach the level of quality of life and healing I wanted and the benefit of the medication far outweighed the possible risks and actually allowed the Autoimmune Protocol to be MORE effective.

What About Painkillers? Can I Still Take Them on AIP?

Note: If you have Inflammatory Bowel Disease (Ulcerative Colitis or Crohn’s) NSAIDs should always be avoided!

NSAIDs or Non-Steroidal Anti-Inflammatory Drugs are pain medications like Advil, Ibuprofen, and Aleve. They work to reduce physical sensations of pain by blocking certain blood inflammation markers and are a less risky alternative to narcotics.

Typically, NSAIDs are eliminated on the Autoimmune Protocol because of their interaction with the gut, increasing intestinal permeability (Leaky Gut) and damaging the mucosal lining of the GI tract with prolonged use ( Considering the amount of physical and emotional stress pain can cause, asking someone to give up the one thing that keeps them going can feel like too big of an ask or just simply isn’t an option right now.

medication and AIP

When Painkillers Are a Good Thing

In addition to eliminating inflammatory foods and adding in healing foods, the Autoimmune Protocol also emphasizes a healing lifestyle. You are encouraged to evaluate your relationships, stress levels, sleep quality, and movement and learn how each of these elements contributes to healing. High levels of constant pain are a big stressor to the body and mind which can severely impact your success with AIP and pursuing healing in general.  

The amount of benefit received from having the energy to plan a nourishing menu for the week, prepare foods ahead of time to make your life easier, enjoy a good night of sleep, move your body on a regular basis, manage your emotional stress, and connect with people you love can outweigh possible risks associated with NSAID consumption. 

Again, it’s important to evaluate for yourself if the benefits of certain medications outweigh the potential risks.

How to Reduce Pain Medication Safely

Note: You should never experiment with reducing or altering medication dosage without first consulting with your healthcare team!

If you are interested in trying to reduce NSAID use, there are a few steps you can try.

  • Follow a healing, anti-inflammatory diet like the Autoimmune Protocol. While you are eliminating inflammatory foods, make sure you are including as many nourishing foods as possible, like bone broth, organ meats, seafood, veggies and ferments.
  • Gradually switch to a natural or non-NSAID pain reliver, like Tylenol. Natural supplements can include curcumin, fish oil, willow bark, or boswellia. This essential oil roll on stick is highly rated for migraines. As always, work with your healthcare team to discern which option is right for you.
  • Don’t just “grin and bear it”. If the pain is unbearable and you need to take NSAIDs, remember that experiencing constant pain is just as much of a stressor and detriment to your healing. Take the mindfully, around meal times and in conjunction with the other healing elements of AIP. It’s also a good idea for anyone on long-term medications to have their liver and kidney function tested once a year.

Own Your Journey

Each healing journey is unique. My sister and I share the same diagnosis but have lived VERY different healing journeys and we’re even related! When you make empowered, informed decisions about your healing, you will never be wrong because you are making the best possible choice for YOUR body.

You can still see tremendous healing on the Autoimmune Protocol while still using medication to manage symptoms. It is also possible that you may want or need to reduce your medication as you see improvements from dietary and lifestyle changes. Just remember to keep an open dialogue with your healthcare team and NEVER experiment with altering prescribed medication doses without collaborating with your doctor.

Disclaimer: Nutritional Therapy does not treat or diagnose disease and should not be used as a replacement for medical treatment. I am not a physician or naturopath and cannot advise readers about how to treat diseases and would NEVER encourage someone to alter medication without first consulting with their healthcare team. Please consult a physician or naturopath if you seek advice about diagnosing, preventing or treating specific ailments.


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.

Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


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