If, in your confusion over what you should be eating with Hashimoto’s you’ve ever gone to your keyboard with furious fervour for answers, you may have received an echoing cry from the depths of the Google realm, ‘you must do the AIP diet!’

You may then have discovered a list as long as your arm of all the foods you are meant to exclude from your diet.

AIP stands for AutoImmune Protocol. It’s a dietary protocol.

It’s intense, it’s restrictive, and for some it can feel like the answer. But for many others, it becomes another exhausting set of food rules that’s hard to follow, confusing to manage, expensive to shop for, and frankly, overwhelming when you’re already running low on energy and mental clarity.

I’ve done it and I’ll be honest, while I did feel better, I remember eating a hell of a lot of sweet potato, spending way more time in the kitchen than usual and feeling hungry and restricted frequently. Keep in mind that I was a Nutritionist in training. Eating out? Going away? Forget about it.

As with many complementary health approaches there is limited research on the autoimmune protocol and Hashimoto’s but some small studies do show promising results with improving thyroid function and participant’s quality of life.

So let’s talk about it, do you really need to go AIP for the best health outcome in Hashimoto’s?

What is the AIP, exactly?

The Autoimmune Protocol is an elimination diet designed to reduce inflammation and help identify food sensitivities that might be contributing to the disordered immune function characterised in autoimmunity. It works on the gut/immune interface, which is an intricate protective system that resides in the lining of your gut wall and is designed to keep you safe from pathogens. The idea being that you are reducing the inflammatory immune response in the gut by removing, reintroducing and therefore identifying offending food triggers.

There is an original AIP diet and a modified version which is slightly more relaxed. You are required to focus on whole foods like vegetables, fruit, meat, poultry and fish. The food is simple although you are allowed herbs and some spices. It’s strict, removing all of the following:

• Grains – wheat, corn, rye, rice, barley, oats, millet, sorghum, buckwheat, even pseudo-grains like quinoa
• Dairy – cow, goat, sheep
• Legumes – soy, lentils, peas, beans, peanuts, chickpeas
• Nightshades – potatoes, tomato, eggplant, capsicum, chilli
• Eggs
• Nuts – including peanuts
• Seeds – including coffee & cocoa
• All processed foods
• Vegetables oils & trans fats
• Food additives – colours, preservatives, flavours, thickeners etc
• Refined sugar and sugar substitutes
• Alcohol

Reintroduction of Foods

Much like the FODMAP diet, the AIP diet has been much abused. It is meant to be a short term exclusion and reintroduction protocol. Think 4-6 weeks or until symptoms subside. However, there are many that stay on it long term. I definitely take issue with that. I got this wrong when I embarked on the AIP too. I stayed on it for over three months and didn’t reintroduce properly. Any diet that removes long lists of whole foods from your diet is going to have negative consequences on your gut microbiome, your relationship with food, not to mention nutrient deficiencies.

After 4-6 weeks of elimination of the above foods you reintroduce each food or food group one by one, with care, while keeping a close eye on symptoms via a symptom journal. This is the stage of the protocol that takes a lot of time and requires a methodical approach. Ideally you would allocate a week for each food reintroduction to ensure you don’t get confused between potential triggers. You might start with a small serve, say one quarter of what you would normally consume. For example, one teaspoon of peanut butter for a couple of days. If you do not notice any reaction you would then have a regular serve of that food on the third day and give your body 2-4 days to ‘speak’ to you about any potential issues with that food. Unlike food allergies which are instant, food intolerance reactions are a slower, inflammatory response that can take hours to days to manifest.

My advice would be to leave the most common triggers like dairy and soy until last. I would not recommend reintroducing gluten as I’ve discussed many times in the blog, it is particularly problematic for Hashimoto’s disease. You can read about that in my blog, Gluten, should you be eating it?.

Reactions can be broad from digestive issues like bloating, reflux, tenderness and disordered bowel motions to neurological, like mood disturbances and anxiety. Fatigue, sleep disturbances, skin rashes, headaches, joint pain, mucus over-production, fluid retention and overnight fluid weight gain have all been reported.

The confusing thing is that your response may be dose dependant. So a tablespoon of peanut butter once a week may not be an issue but a tablespoon every day could be problematic.

When might AIP be appropriate?

So do I recommend it for my clients? Very infrequently. But that doesn’t mean I don’t think it is a worthwhile for some people.

AIP is a helpful tool for those dealing with secondary autoimmune conditions and experiencing intense and stubborn symptom flares. I do recommend it for those with an inflammatory bowel disease like celiac disease and Hashimoto’s because you’re likely to be reacting to multiple foods and it can be difficult to pinpoint what your triggers are.

It can be especially useful as a short-term experiment, when done with proper support and a clear plan for reintroductions. But that’s the key, it has to be short-term and done well. If you go into it already stressed, unsupported, or unsure of how to reintroduce foods, it can just leave you more lost than before. And to be honest, most women I work with just don’t need to go to those lengths to feel better.

The primary reason I don’t recommend it is because it can lead to food anxiety, reduced biodiversity in the gut microbiome and nutritional gaps, not to mention it’s really bloody difficult.

If you just have Hashimoto’s, your quality of life is pretty good and you are able to function, albeit sub-optimally, then I doubt whether the cost-benefit ratio of embarking on the autoimmune protocol is worthwhile for you. I think there is a simpler way. I call it the Thriving Thyroid Meal Method and I outline it in my Food Freedom for Hashimoto’s course.

The case for a simpler approach

Yes, what you choose to eat does make a powerful difference but that doesn’t mean more restriction automatically equals more healing.

I’ve worked with plenty of women who’ve tried AIP, only to end up more confused, more anxious around food, and more burnt out than before. Why? Because when you’re already exhausted and dealing with unpredictable symptoms, eliminating 40+ foods can add stress, social isolation, and even nutritional gaps if it’s not done with care.

And when reintroductions start? Many women panic. Was it the paprika? The almond flour? The smear of butter? It becomes a guessing game that often leads to fear instead of confidence with food. And I’ll bet you want food freedom, not food fear.

Let me say this clearly: if a healing protocol leaves you feeling more anxious, confused or constantly hungry, it’s not the right one for you, no matter how many people on Instagram swear by it.

Identifying food intolerances is really helpful at the beginning of your journey. But it’s not the end of the story. Think of it as removing obstacles to healing. Ultimately you still need to address gut health in autoimmunity and you can do that without super restrictive eating. In fact, a broad variety of plant foods (think nuts, seeds, herbs, grains, vegetables, fruit, spices) each week is one of the most impactful ways you can positively influence your gut health. Remember that any improvement to your gut health and function will also positively impact your immune function as they are intricately connected.

A whole foods anti-inflammatory diet – one that’s gluten-free, blood sugar-balancing, rich in micronutrients, and kind to the gut – can be a gentler and more sustainable path that still delivers real symptom relief and can help with weight loss or healthy weight maintenance in equal measure to the AIP. Personally? Blood sugar regulation did more for my symptoms than AIP and it’s more fun and provides me with way more flexibility than the AIP ever did.

So what can you do instead?

The good news? You don’t need to do AIP to see real changes in energy, digestion, mood, or weight. In fact, many of my clients see significant symptom improvement by focusing on the basics:

• Removing gluten
• Trialling removing soy & dairy the next two biggest food triggers in autoimmunity
• Balancing blood sugar with meals built around protein, fibre, and healthy fats
• Eating balanced meals consistently instead of skipping meals or grazing all day
• Removing or drastically reducing processed foods and inflammatory oils that contribute to inflammation
• Removing or limiting alcohol

This kind of approach isn’t about perfection, it’s about nourishment, rhythm, and realistic changes that actually fit your life. And let’s say you’re still struggling after nailing the principles above? That’s when I would consider a properly implemented AIP dietary intervention.

Keep in mind that AIP doesn’t mean that your blood sugar will necessarily be balanced. The food you are eating may be nutrient dense and anti-inflammatory but if your meals aren’t balances or you’re snacking often, then poor blood sugar regulation is going to have a really negative impact on your gut health.

Final thoughts

If you’ve been thinking that the only way to manage your Hashimoto’s is by giving up everything you love and surviving on kale, liver and kombucha… please take a deep breath.

You don’t have to do it all at once.
You don’t even have to do it perfectly.
And you certainly don’t have to do AIP to feel better.
What you need is clarity, common sense, and support – not more rules.

If you’re already juggling fatigue, brain fog, food confusion and family meals be kind to yourself and start with a simpler approach. My bet is that the vast majority of you will find the AIP isn’t necessary once you’ve got the basics right.

That’s exactly why I created Food Freedom (Hashimoto’s Edition). It’s a self-paced, step-by-step guide to help you transition to a nourishing, anti-inflammatory way of eating that supports your thyroid, stabilises your energy, and brings some calm back into your kitchen by easing your mental burden when it comes to meals with meal plans, simple recipes and straightforward guidelines.

No panic. No food fear. Just real food, real strategies, and a lot more ease.

While AIP can absolutely be helpful for some people (especially those with a secondary autoimmune condition), it’s not the only option for managing Hashimoto’s.