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What Over Two Years on the Autoimmune Protocol Looks Like

Two Years of AIP

Two Years of AIP

Want to know what two years of following AIP looks like?

My two-year AIP anniversary was a couple of weeks ago…

Since I started my Autoimmune Protocol caper, I have learnt so much. About health. About lifestyle choices. About myself. About the prevalence and diversity of autoimmune disease.

And, while I have written a couple of updates in the past (here’s the first one, and the more comprehensive one year number), because the community of AIPers is growing at such a fast rate, I thought a further update may be in order.

Because when you’re starting out on the Autoimmune Protocol, two years seems like a lifetime.

“Don’t compromise yourself. You’re all you’ve got.”
― Janis Joplin

Here’s my biggest learning:

I have learnt that it is possible to put my 20+ years of autoimmune-related illness almost completely into remission by making dramatic changes to my diet and lifestyle.

It’s true. I’m not overstating or exaggerating.

Let me be clear. It’s not gone as in ‘forever gone’.
But it is immeasurably better than it was.

If you are not familiar with my particular flavour of autoimmunity, I suffer from Hidradenitis Suppurativa (HS). It is a hideous, shameful and painful affliction and looking back, it did a real number on me – especially my self-esteem.

Most of the time, I now live free of HS symptoms. That alone is life-changing. But this healing jaunt has given me so much more.

Here are some of the top-of-mind direct changes:

  • One year after periodontal surgery and the very real chance I would lose teeth, my gums were declared healthy and I experienced bone regeneration
  • With a strong family history of bowel cancer and 4 consecutive years of abnormal colonoscopy results, last year my gastroenterologist declared me ‘clean as a whistle’ and no further check-up is required for 3 years. It would have been 5 without my family history
  • My sleep is incomparably better
  • My mood is more constant
  • A clear sense that I am a full participant in life, not merely an observer
  • People actually comment on how great my skin looks (and this is a huge deal when you experienced chronic acne as a teenager and suffer from 20+ years of a chronic skin affliction)
  • a passion for living my life in a way that serves me

A Little History

I spent 9 months in the elimination phase before I started reintroducing foods. And during this time, I was strict. I didn’t cheat. I gave up my beloved coffee. I gave up chocolate. I didn’t touch wine. I ate no eggs.

If I’m honest, unlike some people, I didn’t actually find the elimination phase too onerous. Sure, I would have loved the odd treat, but my mind was very definitely on the prize. And, I think this is because the pain of an HS flare was far worse to me than any dietary restriction could ever be. And that remains the case, even today. I was pretty seriously focused on healing my gut.

You’ve heard of Maslow and his hierarchy of needs? Well, since I’m a bit of a visual type, I thought an AIP Hierarchy was in order.

And, because they say that a picture paints a thousand words, the image below illustrates about where I am on my AIP hierarchy without me having to go into great detail!

Two Years of AIP

Key Learnings

AIP is about SO much more than diet

When you first start down this rabbit hole, you tend to be pretty focused on what you can’t eat. And it’s true, there are restrictions. But, there’s a whole bunch of stuff that you add into your diet, too.

As I’ve already mentioned, the diet bit was pretty easy for me. You get your head around the formula, and you apply it. You build a repertoire of healthy, nutrient-dense recipes you like and you’re off.

But – it’s really, really important you make changes to your lifestyle that support your road to health. And, this takes commitment. Sleep matters. Managing stress matters. Getting outside matters. Spending time with people you love matters. Learning to put yourself first matters.

One of the absolute best ways to tick all these boxes and keep yourself honest is to track it. I keep a simple Excel spreadsheet. I call it my ‘Food ‘n’ Mood Diary’.

Bottom line: a whole-istic approach is key.

You need support, but your experience will be different from everybody else

There are so many ways to get support specific to this protocol. And, of course, I encourage you to spend some time with your nearest and dearest educating them on just why you are undertaking this course of direction.

But there is also an increasing number of AIP specific blogs, Facebook groups and local meetups out there, too. And, of course, there are now health coaches who specialise in supporting your success on the protocol, too!

Just remember that you are unique. What works for someone else may not work for you.

“Be yourself- not your idea of what you think somebody else’s idea of yourself should be.” ― Henry David Thoreau

Bottom line: stick to your guns

Do the easy stuff first

Given the Autoimmune Protocol is about so much more than just diet, where do you start?

My friend Petra form Petra8Paleo gave me a framework for something I had been doing intuitively – Start with the easy stuff.

I can’t emphasise this enough. You’re in this for the long haul (just consider how long you’ve been experiencing symptoms and the time it has taken to arrive at this point!). So it makes sense to pace yourself. Break the protocol down into manageable chunks that work for you.

  • If the diet seems daunting to you, consider signing up for SAD to AIP in 6. It’s a phased and supported approach to the elimination diet (I’m one of the coaches.)
  • If getting enough sleep is an issue for you, consider picking up a copy of  Go to Bed: 14 Steps to Healthier Sleep.
  • If, like me, stress management is your particular area of struggle, set some goals to find ways to better manage your stress
  • Creating a personal morning ritual was transformative for me. So much so, I created a FREE mini eCourse to step you through how you can create one for you, too.

Bottom line: break the protocol down into manageable chunks.

Respect the past but be ‘future-focused’

Looking – with positivity – to the future is a key indicator of health. Even if its not our best character trait, we all know that ‘positive thinking‘ is good for us.

But did you know that one quality most septuagenarians have in common is their future focus?

Not sure exactly what I mean by ‘future focus’? – Give a future-focused oldie a compliment about their gorgeous garden and they’ll be the one saying, “Come back in three years. It’ll be even better!”

AIP has allowed me to become more future-focused. If I can achieve this in two years, imagine what I can achieve in four or five…?

What could you achieve?

Bottom line: Mental attitude matters


I cannot emphasise enough the importance of getting a good nights sleep. Every night.

And by ‘good night’, I mean between at least 7 – 8 hours, preferably more when you are undertaking the Autoimmune Protocol.

Science is realising more and more just how critical our need for sleep is. Sleep is the time when our body regenerates and heals. It’s when the real work happens.

If you do nothing but clean up your diet and introduce a good sleep practice, you will be doing your health a big favour.

And, if you are having trouble sleeping, check out these handy suggestions to improve your sleep patterns.

Two Years of AIP

Bottom line: Make sleep a priority

There will be a sticky bit

Everyone has one. And, let’s face it – this AIP caper takes work. But, I can pretty much guarantee there will be one area of the protocol that is particularly tricky for you.

For me, its managing stress.

We all get stressed.

But it is the way that we manage this stress that affects our health.

If you’ve been following me for any length of time, you’ll know that I’m a master stresser. I even worry about my level of worrying. Pick the health coach with a degree in psychology!

But, I just continue to chip away at it. And, apply my mind to it.

For me, that means undertaking the training to become a meditation teacher and facilitator (if you can’t beat ’em, join ’em!)

Bottom line: This healing caper isn’t linear. You will discover a part of the protocol that is more challenging than the rest

The elimination phase doesn’t last forever (and isn’t meant to) but your investment in health will never be over

It’s true. Just when you get your head around the fact that the sacrifices you’re making on the elimination phase of your protocol aren’t forever (and in fact, in the greater scheme of things, they’re not even for that long), you realise this is a lifetime deal.

Have you heard that expression, “You can’t go back to holding hands”?

Well, in this instance, you’ll realise that you can’t ever go back to that state of blissful ignorance you had before you started AIP. You’ll always be a label reader now. You’ll always want to talk to the farmer about what he feeds his animals. You’ll be the one walking the perimeter of the supermarket. And that’s if you actually go to the supermarket anymore. It will just matter to you.

And that’s 100% ok!

Bottom line: AIP will change your life. For the better.

Dolly sums it all up best, I think:

“Find out who you are and do it on purpose.”
― Dolly Parton

One of the ways I live my AIP way of life – especially when I hit a sticky patch – is to take things back to AIP basics two or three times every year. It’s a great way to (re)find my AIP groove.

Come and join me on the next 30-day AIP Reset with fellow AIPers who are recalibrating…Two Years on AIP

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Comments (31)

Thankyou for writing this. It made me look at myself differently than I was. I have been on AIP now for over 3 yrs. A lot of my symptoms have gone but a few still remain. Blood tests have improved remarkably as well.I’m not tired and sick any more like I was 3 yrs ago and I can do so much more now, I don’t have awful bad days like I used to, I couldn’t even dig in my garden back then. I know now that I can’t expect to be 100% well tomorrow when it took me 52 yrs of incorrect food and lifestyle that were not right for me but in time my health has improved and I know it will keep on improving but not without effort. It has amazed me that so many natural foods that I have always eaten my body does not like and I react to, even some safe foods on AIP like sweet potatoes and avocados or many fruits. I have not cheated at all as I have seen the benefits and that has made it easier to stick to. I grow a very large proportion of our vegetables and herbs and have increased the garden area as I have improved my health and energy. So I will wait and watch and slowly I will keep trying the food reintroductions as my body allows. It’s just a matter of time.

Lorelle – thank you so much for taking the time to comment.

I’m so pleased that AIP has been so transformative for you, too. I feel exactly the same way – it took me an awfully long time to practice my bad habits (including being an avid smoker for a couple of decades), so when I consider that – its incredible what 2 years dedicated to this protocol has achieved! I look forward to where I could be in another year…

Like you, there were ‘approved’ foods on the elimination that I discovered didn’t serve me – carob was one.

Congrats on your 2 year anniversary of the positive health journey Jo! That’s a brilliant achievement. And here’s to the next 2 and more. 🙂

I saw my GP yesterday and he reminded me just how far I have come in 10 months. Like you, I don’t find the AIP too onerous but I think that is because I like cooking and I have a very supportive partner who basically follows the protocol with me. He tries to remind me that he doesn’t need to, and I remind him that he didn’t need to ‘yet’, but this way he will thankfully probably never get to that point. And we’ll live to a ripe old age together fully able to enjoy it.

AIP will be in my future forever, and that’s okay by me. I do miss a few things, but only when I see them. Like if I see an ad on tv for Magnum iceceam I do then miss it. Or if I watch a film that has chefs and cooking in it… my fave sort of film, I often miss what I can’t have. But if I don’t see it, most of the time I don’t miss it.

PS I like your variation on Maslow’s heirarchy but I wonder if it is upside down?

Hey lovely Melanie – you have an AWESOME partner! AIP will be in my future forever too – and, I’m completely OK with that. Especially when I see how far I’ve come.

I don’t think my hierarchy is upside down, for me! The maintenance phase is the bare minimum for this AIPer (and I think everybody should find ‘their’ whole food version of it). Some of us need to become more enlightened through a stricter process…

This is a FANTASTIC post Jo – thank you for sharing it with us.

I’m so glad you have healed so much, to be nearly free of HS must be an incredible relief and is testament to your hard work and dedication. I agree with you, AIP is much more than just nutrition – it’s the lifestyle and mindset factors which can make our break the speed of our healing.

One question – What does Bella think of Boris?!

Lovely Rory – AIP brought our friendship!

Bella doesn’t even register Boris (nor Boris, Bella)!

Great post Joanna! I feel the same about the elimination phase. I really didn’t struggle to give up anything either – it’s all about having your eyes on the prize! No only does that prevent you from cheating, it also means that all your positive thoughts and energy is going into believing that you will get better! x

Hi lovely Stella! Thanks for stopping by, Possum.

I wonder where the next year will take us…?

This is a wonderful post Jo, I love the way you see your journey so far and also your zest and enthusiasm for what’s to come. I shall be celebrating my two years next month and can also say my life has changed immeasurably. Not only with how I feel but how I think, just like you. Here’s to more knowledge, onwards and upwards!
Btw I just want to say how much I love that top photo – you look positively radiant, Possum!! x

Kate – one of my most favourite things to come out of this AIP caper is all the fab’ people I have met around the globe. That’s you, Possum.
It is so wonderful to me, that life can gift you with these unexpected bursts of pleasure.

Outstanding post my dear friend, honesty prevails, you continue to inspire with your Frankness Frankham!

I think the ‘frankness’ is integral to the ‘Frankham-Ness’!

Grateful for our friendship, TBM!

Hope. That’s what I feel when I read this. Thank you. I’m just beginning a stroll down this path. And it’s not a path I would have chosen, but there is beauty along the way. And you are one of the gorgeous flowers on the side of the road. Blessings!

Margaret – you have just officially made my day with your gorgeous comment. Thank you.

There is beauty along the way. More than you imagine when you are starting out (although I see you have already come far).

Many blessings back to you.

Yay, Joanna! You’re a rock star~.

I suspect there’s a little bias there, Petra. But thanks, Possum!

You are such an inspiration to others like myself on this AIP journey. I agree with you 100% that its good to take it in steps if need be. In fact it would be impossible to jump into EVERY aspect of this life change in one day (there’s so much to it…good stuff…but a LOT of good stuff to learn).
I always forget to use my EFT. Duh. When I was doing it daily it was helping, as its a meditation + stress therapy for me. Thanks for mentioning it…I;m going to hop right back on the EFT train.

Hey Samantha – Thanks for your gorgeous message, Possum!

I’m new to EFT – which kind of very loosely combines ACT (Acceptance and Commitment Therapy) with acupuncture; two things I am familiar with. I have to say, I’m surprised with how much I am enjoying it. I’m getting my tap on every day and it’s kind of groovy!

Hi Joanna. My name is Brynn and I have had HS for almost 20 years now. I’m “Stage 3”. I’m wondering if you have any wisdom to impart in regards to your HS and how AIP has helped with that. I’m nearly ready to try anything at this point. Thank you.

Hi Brynn – you have my sincere sympathy. Stage 2 HS was no picnic, so I can only imagine how life is for you at Stage 3.

I was ready to do almost anything to mitigate my HS symptoms, so I jumped into the full AIP elimination head first. Having said that, I had already determined that gluten was not my friend.

Two life-changing books for me were Tara Chester-Grant’s, “the Hidden Plague” and Dr Sarah Ballantyne’s, “The Paleo Approach”.

Given it’s nutrient dense focus, AIP will help with stabilising hormonal dysregulation (often an issue for those of us with HS). I remain on a soy, grain and nightshade free diet (except the odd white potato) and only eat a little high quality dairy. Anecdotally, nightshades are often problematic in our community. I can say that supplementing with zinc has been helpful for me. I have worked hard to improve my sleep and mitigate stress (which is an ongoing issue). I’ve also become a bit of a fermentation queen.

Of course, I’m very happy to talk further with you – drop me an email via my contact form if you’d like to arrange a Skype call. One of the biggest discoveries for me was just how important support is. Here to help.

This post was a very enjoyable and motivating read. I could write an ode to sleep! I’ve suffered with sleep problems for years and on this vacation, one month of travel in our camper through the US southwest, I have rediscovered the 10 hour sleep. Amazing! I am not cured of my ills but at least I feel present all day until I blissfully fall asleep again.

Hi Cteachr! – I’d fancy reading your ode to sleep, Possum! Isn’t it profound when you understand just how much brighter the world can be when you’ve got enough sleep in the bank?

Wow, you are the only person i have heard of with this besides a friend of mine. Sadly she died too young. We both were trying to figure out healing our chronic debilitating illnesses and she passed away before i got the answers
:(. I had health issues my whole life but lyme was the tipping point i almost didnt think i could bounce back from. Thankfully through determination and persistance and the will to keep fighting i did a lot of research and everything came back to diet, environment and lifestyle. I actually do a very strict diet a little more so then AIP because of what works for me. I Have really learned to listen to my body. I even make most of my own household and personal products. Its changed my whole life and honestly i wouldn’t trade it all for what i have learned. I am thankful for family and a fiance that have been helpful and supportive. And grateful to have access to resources such as books and documentaries and support groups that opened my eyes to a journey of healing. 🙂 i wish it was easier to reach out to everyone with health issues and let them see there is hope and options for recovery.

Kim – thanks so much for sharing your story.
I agree – I wish it was easier to reach out, too. I think it’s improving, though. As more and more of us experience positive change through improving diet and lifestyle choices, word is getting out.

I am so sorry to hear about your friend.

Catharina Delmarcel

Ho Jo, awesome post! I couldn’t agree more with all of your bottom lines (nor the quotes 😉
We’re entering this new stage called long term AIP and it’s important to have some people guide us there as well. 2,4 months in, I’m still learning – and loving this journey. xxx

It’s become my baseline, Catharina – and, it has brought me so many new ‘global’ friends… 🙂

Hi, Thank you. I’ve got a supportive partner who does all our cooking, I’ve been on AIP for three months but unlike you I have slipped up. I have exactly the same family history of bowel cancer as you, so nice to know AIP will also be of benefit to that and to my Hashis.
My problem is I have slipped up. Twice with caramel sslice. Once with spaghetti and I have one coffee a week. I usually pay for it. Most of the time it isn’t a problem
I am interested in your option on the posts I have seen recently that say you shouldn’t stay on AIP for too long or you will become allergic to foods your body would otherwise accept :). Bit confused as I was happy to go along with this diet as is (with my occasional slip up).
Thank you

Annette – I’m glad to hear you have the support of your partner. It can make all the difference.

I do not subscribe to this theory. AIP is a nutrient-dense protocol. I will say that you should definitely ensure you’re eating enough variety – especially by way of vegetables, though.

Thanks for the encouraging post. I am new to AIP, I’m a month in to the elimination phase. However I have really struggled, I didn’t look into what I could have and apparently didn’t look over what I couldn’t have very well. I was eating 2 foods almost daily that I wasn’t supposed to. And my food options were pretty awful since I didn’t seek out recipes. I am now pretty much starting over and scratching the last month. I still find this entire process very overwhelming, but I’m going to make my best go at it.

Hi Jessica – thanks for stopping by!

AIP is a whole new way of approaching our diet and lifestyle. There is no doubt it requires planning and self care in a way that modern living down’t prepare us for. My advice to you, especially at the beginning is to keep it very simple. Focus on getting the basics right – nutrient density, especially. Batch cooking is your friend.

Here if you have any question! Good luck!

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