Autoimmune protocol

The Autoimmune Protocol

My passion for autoimmune disease stems from my own personal battle. For many years, I suffered from a hormonal imbalance known as hypothyroidism. I experienced symptoms such as hair loss, constipation, weight gain, irregular menstrual cycles, brain fog and chronic fatigue. My doctor agreed that my thyroid was not functioning optimally, but chose to take a wait-and-see approach while my health continued to deteriorate. I decided to take my health into my own hands and seek out a naturopath, who eventually diagnosed me with Hashimoto’s Thyroiditis.

I started taking natural desiccated thyroid (NDT) medication and after a few months, began to feel like myself again. But the thought of relying on a pill for the rest of my life didn’t sit well with me. And I knew that medication was only a band-aid for what was really going on in my body. I researched holistic alternatives and stumbled upon The Autoimmune Protocol. I discovered that genetics wasn’t the only factor in autoimmune disease, and that diet and lifestyle were two major components.

While I couldn’t change my genes, I had complete control over what I ate and how I lived my life. It never occurred to me that the healthy whole grains and legumes I consumed were contributing to the problem. Or that the two jobs I was working to put me through nutrition school could be affecting my gut health. In the same way that diet and lifestyle can contribute to autoimmune disease, they also play a key role in the body’s ability to heal. By giving your body a clean slate, you can halt the progression and even reverse autoimmune disease. 


What is the Autoimmune Protocol?

The AIP is a diet and lifestyle protocol, designed to bring your body back to balance over the long-term. It helps those suffering from autoimmune disease discover their environmental triggers. As well as determine food sensitivities, reverse nutrient deficiencies, balance hormones, restore gut health, regulate the immune system and support overall healing. While there is no cure for autoimmune disease, following the autoimmune protocol can get you back to health and put you into remission.

In general, the AIP diet involves eating nutritionally dense foods and removing those that are most likely to be problematic. Whole foods such as organic fruits and vegetables, bone broth, wild-caught fish, quality animal meats and healthy fats are added to promote healing.

Foods that trigger an immune response, irritate the gut and cause inflammation are removed. These include dairy, soy, eggs, nightshade vegetables, nuts, seeds, legumes, grains and food additives. After the elimination phase, foods are re-introduced slowly and systematically. This helps to identify which foods are not well tolerated and may be triggering your autoimmune disease. Over time, you will be able to build a life-long diet that is tailored exactly to your needs.

The autoimmune protocol also addresses lifestyle factors that may be affecting your autoimmune disease. Getting good quality sleep, managing stress, making time for hobbies and connecting with nature can be just as important as eating a nutrient-rich diet. Moreover, these changes are something that you have to figure out on your own. For you it might be best to focus on sleep, while someone else might need to focus on improving their environment.


Since the AIP diet provides all the necessary nutritional requirements, some people may also benefit from the use of supplements. It’s important however to check the labels carefully, as supplements are often derived from common allergens like wheat, corn and dairy. Look for statements like “certified gluten-free” and avoid ingredients that may trigger your autoimmune disease. Some practitioners recommend herbs to help reduce inflammation, modulate the immune system and combat stress. While this can be incredibly helpful for some people, it can be like playing with fire for others. I recommend working with a knowledgeable practitioner such as a Holistic Nutritionist (RHN/CNP) or Naturopath, to determine what’s right for you.


Diet Breakdown

This diet is not ideal for vegans or vegetarians, since it eliminates most of the plant-based protein sources. I personally didn’t feel like I could get adequate nutrition or maximize my healing potential without following the protocol completely. One of the things that helped me accept this, was knowing that I could still make ethical food choices.

I spent some time getting to know my local grocers/butchers and the farmers they source their animal products from. I always ensure that the meat I buy comes from animals that have been humanely raised and that fish is wild caught and sustainably sourced. This is important to me from both an ethical and health stand point and is a big part of the AIP diet and lifestyle.

A typical day for me on the AIP diet looks like this:

  • Breakfast – a low glycemic fruit smoothie (such as raspberries and blueberries) with spinach, coconut oil, collagen protein and coconut milk OR sweet potato toast with a matcha latte
  • Lunch – homemade grass-fed beef , lamb or turkey patties with salad greens, avocado, cucumber, radish, beets, carrots + olive oil, lemon & apple cider vinegar dressing
  • Dinner – grilled wild salmon or organic chicken with roasted vegetables (sweet potatoes, broccoli, cauliflower, cabbage, or turnips) and sauteed dark leafy greens (kale, swiss chard, or collard greens)
  • Snacks – homemade bone broth, gelatin gummies, coconut yogurt, apples or veggie sticks with tigernut butter

I will reserve treats for once or twice a week (or special occasions) and they include things like carob chocolate, cassava tortillas, AIP muffins and tigernut cookies. I do my best to hide organ meats in my burger patties every week. I flavour everything with AIP compliant spices. I also do batch cooking once a week to help me save time in the kitchen.



Addressing lifestyle factors

The lifestyle component can often be the most difficult to address on the autoimmune protocol. It’s easier to change your diet than to switch careers, manage stress or ditch a toxic relationship. But no matter how ideal your food choices are, you won’t experience healing without making the necessary lifestyle changes.

Practicing stress management techniques, spending more time outdoors, getting quality sleep and meditating are just a few of the lifestyle factors I have focused on since going AIP. I engage in mild-moderate physical activity that supports my body in a positive way. This can include yoga, stretching, walking and biking. High-intensity exercise can be counterproductive for those with autoimmune disease. It may not only slow healing but exacerbate your condition.

There are many great blogs and resources out there with tons of AIP recipe tips and inspiration! Some of my favourites include:

References: MindBodyGreenThe Paleo MomAutoimmune Wellness

To learn more about gut health, click here.


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Gillian is a Registered Holistic Nutritionist and founder of Wholeheart Nutrition. After a long journey with autoimmune disease, Gillian is passionate about helping others with chronic illness. With a holistic approach, she coaches her clients on their path to healing through diet and lifestyle interventions. Gillian writes about her experiences on her blog, in hopes to support others on their own wellness journey. When she’s not working with clients, you can find her dreaming up healthy recipes in the kitchen or practicing yoga at Studio Blue in Toronto.