Five things to expect on the Autoimmune Protocol

The prospect of cutting out so many foods doesn’t exactly make the AIP the most exciting or inviting diet to try. The difficulties of any diet can be discouraging but the list of ‘don’t eats’ seems so ridiculously long on this protocol that anyone who has never adhered to any such restrictions might feel a little terrified at the idea of not eating grains. You truly believe that you’re going to starve.

For me, getting started wasn’t too difficult but it wasn’t plain sailing either. To begin with I totally dismissed the idea that I wasn’t even allowed to eat homemade bio yoghurt, which is necessary to the similar(ish) Specific Carbohydrate Diet that I had experimented with for a month beforehand. After some serious reading I soon accepted how real the science behind the AIP is and how religiously you must follow it.

For the past four years I have been following a wheat-free diet to alleviate what I thought were symptoms of IBS or possible gluten intolerance. I had a few cheats along the way with very occasional traces of wheat found in foods such as sausages but in general this restriction massively helped with the chronic diarrhea I suffered. However, let’s be clear; wheat-free or gluten-free is not enough to fix an autoimmune disease. My undiagnosed Crohn’s disease soon caught up with me and forced me to face a harsh reality: eat clean or face surgery. So, from the perspective of already being accustomed to a wheat free diet and taking into account the absolute necessity of changing my diet, going AIP wasn’t that difficult… for the most part.

The biggest struggle I faced was not eating sugar. If overindulging in sugar were a criminal act I’d be facing a life sentence, locked up in solitary confinement and imagining that cockroaches were medjool dates. I’m the girl that would happily eat a whole Easter egg in one sitting and then consider buying another. In February. Well, if a candida die-off can be considered the penalty, I certainly paid it. Which brings me to my first point regarding the five things you can expect to experience when beginning the Autoimmune Protocol:

1. Candida Die-off

This is also known as the Herxheimer reaction – a bad bacteria “die off”. Candida Albicans is a type of fungus or yeast that forms part of the gut flora. When out of control it can weaken the intestinal wall (contributing to that leaky gut I told you about) and release toxins into the bloodstream that eventually provoke your body to attack. But how does candida get out of control? It thrives on a diet rich in carbohydrates and sugar. When you cut out high-carb foods and sugar you essentially starve these bacteria and cause them to die. As they die they release their endotoxins into the body faster than the body can cope with them – this can cause many side effects such as nausea, headache, fatigue, dizziness, sweating, fever, night sweats, chills, bloating, gas, constipation or diarrhea, increased joint or muscle pain, elevated heart rate, rashes and skin breakouts. Taking or eating probiotics to outnumber the bad bacteria with good bacteria and also popping anti-yeast supplements such a grapefruit seed extract can exacerbate this die-off. I did all three of these and pretty much bombed out those pathogens but it left me with some serious night sweats, fatigue, headaches, diarrhea, etc. and lasted for about 2 weeks until my body adjusted. It is better advised to change your diet first and then think about introducing probiotics later to ease your body in.

2. Fatigue or Low Carb Flu

Your body has learned to burn sugars and grains (carbohydrates) as fuel for energy. It’s exactly this type of diet that causes insulin spikes, glucose levels to drop and sends out hunger cravings just 90 minutes after eating. You body now has to unlearn this pattern to become a fat-burner. As your metabolism shifts and learns to use fat for fuel you may at first experience fatigue, lethargy, headaches, intense food cravings (usually for sugar but sometimes for fats), mood swings, depression, anxiety, malaise, and even stomach and digestive upset[1]. I didn’t feel this too badly because I think I over compensated by eating A LOT and Dr Sarah Ballantyne emphasizes that it’s important to stay hydrated, eat quality fats, exercise and sleep well to help with this. Whatever you do, don’t give up. This will pass within 2-4 weeks. Once your body has readjusted you’ll soon have more energy than you did before! One thing to note here: the AIP is not a no-carb or a low-carb diet; it’s just not a high carb diet. You will still get carbs in the form of fruit and vegetables so don’t go totally eliminating all fruit sugar, just keep it to a minimum. Have a read of this article on Sugar Burners vs Fat Burners:

3. Weight Loss or Gain

I lost a stone in weight (6.35kg). I was a little worried about this as I was already slim to begin with but I can confidently say that my weight has stabilized and I am perfectly healthy. The weight loss can occur at the beginning of the diet because you’ve suddenly cut out carbs that your body is so used to burning. I noticed each week I was losing more weight but this eventually plateaued and I have remained at the same weight for the past few months. Some people have even reported weight gain (particularly those suffering with malnutrition or diarrhea prior to the diet) because finally their bodies are retaining much-needed nutrients. I imagine this happens much later into the diet when the gut has healed enough to stop causing such severe gastrointestinal reactions. The key point to remember is that being a healthy weight will better enable your body to heal and manage inflammation. Hormones and lifestyle also play a huge role in weight loss or gain so I recommend reading pages 275-277 of The Paleo Approach.

4. Mistakes

You will, without a shadow of a doubt, make mistakes. The AIP is a lot of information to take in and you can’t expect yourself to remember every single do and don’t at the beginning, especially when eating out. Don’t beat yourself up over it. Try to let go, learn from the experience and make the right choice next time. You’ll soon get into the swing of it. I remember I ate tomatoes with my salad because I forgot they’re a nightshade. Easy mistake, they’re Paleo after all. It’s important not to become ‘orthorexic’ and live in fear of what’s on your plate but you still want to be careful. Don’t be afraid to ask friends and family what ingredients they’re using or ask the waiter whether something is gluten free or contains dairy if you suspect it might. Better to be safe than sorry, but don’t be tormented by it.

5. Be Patient

All good things come to those who wait. Don’t expect an overnight cure. You’ll still find just as much hair at the bottom of the shower tomorrow (if you suffer with AA) and there’s no guarantee your gastrointestinal discomfort will disappear after your next meal if you’re suffering with Crohn’s. Do stick to the diet for AT LEAST 30 days. The length of time it takes to heal varies from person to person depending on the level of damage in the body. To allow for healing of the gut to take place and therefore repair throughout the immune system and entire body (your hair if you have AA), a minimum of 30 days can be enough to show some improvements but 3-4 months is a much more realistic time scale to allow for the body to truly start rebuilding itself. Anywhere along that timeline will be where a person has rebuilt their body enough to see improvement in autoimmune symptoms.

Remember, the AIP is more than just a diet. Exercise, sleep, relaxation and other therapies are all necessary and conducive to healing. I’ll write about my experience with those another day but for now I urge you to read Dr Sarah Ballantyne’s book The Paleo Approach and blog to get the most out of this protocol.

If you have any questions or suggestions for future blog posts, please do let me know.

p.s. video below!

Good luck!


[1] S. Ballantyne (2013) The Paleo Approach. USA: Victory Belt Publishing. Pg. 269

*If you find this blog helpful and you like to see more content from me, please consider a donation. The funds will help pay my tuition fees at the College of Naturopathic Medicine so that I can become a Nutritional Therapist and thus be better able to help you.*



14 thoughts on “Five things to expect on the Autoimmune Protocol

  1. Hi Stella,

    Firstly I just wanted to say that your blogs and youtube videos really inspired me to get healthy and make me realise that I can heal my own body. I think it’s great what you have done to help others.

    I am currently suffering from quite a bad case of Alopecia Areata quite like how your hair loss was. As you know it is so distressing but I am determined not lose all my hair !! I have been on the diet about 7 weeks now and still seem to be losing hair. However i am getting more regrowth. I just wanted to know how long was you doing the diet before you started to notice your hair had stopped falling out? And I know everyone is different but how long do you think I should keep up the diet as strictly for ?

    Thanks !


    • Hi Jessica,
      That is awesome! I’m so glad you’re feeling inspired 🙂
      I think it was maybe 2/3 months into the diet that my hair stopped falling out. As you say, everyone is different. I waited about 5 or 6 months before taking baby steps with my reintroductions each month. I’ve only just now completed finished with AIP. I think you should keep things up strict until it’s clear to you that your hair isn’t falling out and your regrowth is strong. xx


  2. Hi Stella, very glad you have posted about the die off. I’m a few days into the AIP and I honestly feel terrible, bad headaches and brain fog, really fatigued (I can hardly drag myself to work, but then I do walk a long way to and from work), night sweats and feeling really quite down 😦 Now I can see from your post that this is relatively normal in the first stages and that I should just keep going. Is there anything I can do to help myself a little?


    • Gosh it can be very off putting right?! I promise it will subside! Are you taking probiotics at the moment? If so I would recommend lowering your dosage so for example take it every other day rather than every day – same with foods if your consuming those. It’s also a good idea to just focus on the diet at the beginning and only later introduce probiotics once your settled and running well with the diet. A little at a time is the best way to do it rather than bombing yourself out. x


      • Thanks Stella. The die off subsided like you said, just had to stick it out. I wasn’t taking probiotics at the time. Can I get you thoughts on exercise? I currently walk about 7.5 miles a day, to and from work. So that’s 2 hours moderate walking spread over the course of the day. Its not particularly strenuous but I am wondering whether I should consider this excessive in terms of AIP? Its very normal to me but I don’t want it to ruin my healing. Do you think I should reduce this?


      • Oh I’m so glad you stuck it out! 🙂 Walking is the very best exercise you can get so I don’t think that’s excessive at all. As long as you’re not feeling drained/pushing too hard while you’re doing it. Or feeling stressed for that matter! x


  3. Hi there, I found you through Youtube. Nice to see that you’ve managed to target your issues and heal with AIP. I’ve been dealing with some patchy alopecia this past year which has been stressful as you know. I have been gluten-free for several years after discovering I was gluten intolerant so I doubt that gluten was a contributor to my hair loss, but I’m following along with AIP to see if it might help. Haven’t consulted with a doctor because I don’t have insurance, nor do I really believe they’d target anything other than the symptoms.

    My question for you is, how long did your alopecia last from beginning to end, if you’d considered it having run its course? Two questions actually; did you feel ravenous when starting AIP and did that eventually subside? I used to rely upon eggs to keep me full through noon and I’m finding breakfasts really challenging, also without sweet potatoes which seem to give me a blood sugar crash an hour or two later.

    Thank you for reading!


    • Hi Nelly,
      I’m not sure what you mean by how long did alopecia last from beginning to end? Alopecia areata is an ongoing disease. Some people may experience recurring patches and regrowth their whole life, some people only get one bald patch once and never again. Everybody is different. I personally have had this condition for 4 years. I have had at least 2 patches at any given time while other have been growing back.

      I didn’t feel ravenous on the diet because I made sure that I had plenty to eat. Some people feel that way at first but yes it does subside. Before the AIP when I used to eat a standard diet I would be hungry all the time and could barely make it to 11am without snacking after breakfast. That’s because carbohydrates like wheat, potatoes, rice are metabolised very quickly and leave you feeling hungry again. Meat and vegetables take longer to digest and I now find I can go for hours without eating and not feel ravenous.
      Why don’t you try eating avocado instead of eggs for breakfast?


      • Thanks for the reply. I’m new to all this so sorry about the confusion around my question – I guess I got the impression through your YT vids, and given the contrast b/w the first video and the most recent (major hair loss vs it all growing in), that your Crohn’s and AA to had gone into remission thanks to the AIP diet.


  4. Hi Stella, great post and really informative. Just the boost I needed, I started the AIP diet about 4 months ago, after 3 I started to eat potatoes, gluten free oats, sheep cheese and yogurt and some white rice (oh and worse of all dairy free chocolate). I got fed up because I wasn’t seeing any results at all!! My hair got worse and worse every day, handfuls were coming out, I touch my hair and am left every time with loads of hair in my hand. I have probably lost about 90% now and with the tell tale spikes running through the rest I don’t think it will be long until I’ve lost it all :0( I’ve been so low that sticking to the diet has been a massive struggle. I HATE sweet potato and being a former veggie I can only stomach chicken or limited fish. I miss eating ‘properly’ I love potato!! I used to eat a lot of quorn but since being on the diet I have found out I can’t eat eggs! So when I tried quorn mince which contains egg whites I had a serious upset stomach for 3 days!! I don’t know how you do it, I get so hungry! Bone broth.. I don’t think so!!

    Help!! Suzanne x


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s