#3 Start Here – Digging Deeper & Troubleshooting

Blueberries and Daisy

Unfortunately there may come a time when you feel it’s one step forward and two steps back. In cases like this you might want to dig a bit deeper into the do’s and don’ts and do a little troubleshooting.

I’m going to get on my soapbox here for a moment here,
so brace yourselves!

TRACKING – There is a REAL need for proper tracking and monitoring to know what’s working and what’s not. By tracking, I mean everything we consume, what we do daily (work, sleep, exercise, relaxation, self-care), our stress levels, reactions to food, medications and more – this can be more than just an upset tummy so if you’re not sure what else this may include, read up on reintroductions (even though you may not be to that stage yet), things to watch for include itching, skin problems, dizziness, pain, congestion etc. I call this type of tracking a food/mood/poop journal, and yes, it is a real thing! If you’re not doing it, I highly recommend you look into it (one of these days I’m going to write a post about it), but for now you should know a few things:

1) Reactions to foods, supplements, etc. can happen up to 72 hours later (trust me – you’re not going to remember this type of detail 3 days later unless you journal it!),

2) While the AIP is NOT about weight loss I highly recommend you weigh yourself every morning and keep track of it – reactions can come by way of subtle inflammation, and weight fluctuations can help you pin-point your triggers,

3) You don’t need to buy anything fancy or find some special app for this – I used an Excel spreadsheet and kept it in the cloud so I could update it on the go. The best part about a spreadsheet is it’s searchable, so I could easily look back when exploring problems and reactions.

GIVE IT AN HONEST SHOT – It’s only by truly giving the Autoimmune Protocol your full attention that you’ll really know what’s working and what’s not. The Elimination Stage is 30 days minimum, but 60 – 90 days is not uncommon before most see marked improvement in symptoms. Don’t expect miracles … slow and steady wins the AIP race. IF after giving it a REAL and HONEST shot you’re not seeing seeing the improvement you expected it is time to start the troubleshooting process as you may be dealing with underlying issues that you may need professional help to get to the bottom of and start treating. Please be sure to check out my post – Finding Your Root Cause where I provide an abundance of information about getting to the bottom of yours.

DID YOU REALLY? – I hate to be a nag, but did you REALLY give it an honest shot? Did you really follow the protocol properly?  First and foremost, if you’re struggling but have never considered The Autoimmune Protocol book by Dr. Ballantyne, I will again suggest it to you. Not only does she include information about the basics and reintroductions, but she includes troubleshooting as well. If you’re honestly ready to start troubleshooting, keep reading.

Do’s & Don’ts

I’ve saved this until part three because I really want you to keep it simple starting out, and because, let’s face it, nobody wants to be faced with an even LONGER list of restrictions and directions after trying to adjust to the foods allowed and omitted. This article by Dr. Sarah Ballantyne, AIP Do’s and Don’ts (click for article), is an amazing compilation of issues she’s helped people like us work through on their healing journeys. There are almost literally a bazillion links to other articles shared in her post, so if you’re not feeling up to digging really deep at this point, be careful to look at this with a more high-level or basic approach – read the introduction and them simply consider each numbered headline and assess whether it’s something you think might be one of your pitfalls, something you’re skipping or not giving enough attention to on your journey. Once you determine your weaknesses, look further at those as a starting point – don’t read items that don’t apply to you, this will only cause yourself overwhelm and confusion.

Progress & Patience

From time to time you’ll hear people mention “detox,” “Herxheimer” “withdrawl” or “die-off” reactions when you begin the elimination stage of the AIP – and if you’re feeling worse than before you began, you may be scared or want to give up. I suggest taking a look at this well-written post  – Is a Healing Crisis Really Healing?

If you’ve been on the AIP a while and you think it isn’t working or feel your healing journey has stalled, be sure to read – How to Gauge Success on the AIP When Progress Isn’t Obvious.

Another common pitfall is our own impatience, and who can blame us, we just want to feel better! check out Eileen Baird’s article here – Is Your Impatience An Obstacle to Healing?

Maybe you feel like you’re taking one step forward and two steps back? If you’ve seen some progress and are discouraged because you feel like you’re backsliding, you may just be suffering a temporary flare. I personally have to remind myself of this frequently! I’ve been on my personalized AIP for quite some time and I start to think as though I’ve come this far, surely there should be no going back. Unfortunately, that’s simply not the case and from time to time we’ll face a flare of symptoms for one reason or another. If that’s you, check out this very helpful article – Autoimmune Flare Self Care.


Probably the best article I’ve read on this topic is written by Mickey Trescott of Autoimmune Wellness. She delves into when you do and when you don’t need to troubleshoot, first steps to troubleshooting, three areas to explore and her own personal experience troubleshooting the AIP. Click here to read the full article – Troubleshooting the Autoimmune Protocol – A Guide.

Professional Help

If you’ve come this far and still don’t know where you’re going wrong, I highly recommend you consult a Functional Medicine Practitioner or Certified AIP Health Coach so that you are sure to address any underlying issues. Without getting to the root cause of your illness, the AIP can feel a bit like putting a band-aid on a battle ship!  Click here for where to find professional help and even a list of Paleo-Friendly Autoimmune Specialist MDs.


NOTE:  As with any significant dietary change, you should in fact have only undertaken the AIP at the recommendation of a trained nutritional coach or physician.