When I told Lily I thought I had the perfect diet for her, she was confused.

The word “diet” immediately made her think of weight loss, but she hadn’t come to see me for that. In fact, she was quite thin! What brought her to my office was chronic pain, aching, low energy, exhaustion, and uncomfortable GI symptoms she experienced due to an autoimmune condition.

I had to explain that when I say “diet” I’m talking in general terms about what we’re putting in our bodies. Diets for weight loss are a totally different subject.

Lily, like so many women who are living with an autoimmune disease, was frustrated and confused.

Her doctors had told her there wasn’t much to be done; they could manage the disease with medication, but there was no cure. She’d just have to learn to live with the symptoms, modifying her daily activities to minimize the pain.

She came to see me because she wasn’t willing to resign herself to an inactive lifestyle. She’d spent much of her life hiking, biking and enjoying the outdoors. How could she give all of that up?

During our initial consultation, I asked Lily a lot about how she ate. As I listened, I could see some adjustments she could make that might change everything!

That’s when I told her about the autoimmune protocol. It has nothing to do with losing weight (though for some, that’s a happy side effect) and everything to do with feeling your best!

The autoimmune protocol (AIP) can seem fairly restrictive when you first start. But after a while, you’ll get so good at using whole foods creatively, you’ll realize there’s a ton of flexibility. You might not even miss the old choices that you leave behind!

And honestly, isn’t a restricted diet better than taking medication forever or having to stop doing your favorite activities? I certainly think so!

Let’s take a look at what the AIP is, how it’s similar and different from Paleo or Keto diets, and how it impacts the uncomfortable symptoms of autoimmune disease that are likely a result of hormonal imbalances. Then, I’ll give you some tips for incorporating the AIP way of eating into your life.

Autoimmune Protocol, Paleo and Keto

Every woman is unique, which is why even when two women have the same condition, the way their bodies react may be totally opposite. With autoimmune disease, the symptoms you feel vary depending on other factors, such as whether your hormones are in balance or you have unknown food sensitivities, to name just a couple.

That’s why I never say one particular way of eating is best for everyone. It’s simply not true! That’s why I take the time to research many different options so I can recommend the most sensible plan for each woman’s circumstances.

AIP, Paleo and Keto all have some similarities – and some big differences. Let’s take a quick look at the basic premise of each, then we’ll talk about how to choose which may be the solution you’ve been looking for.


The general idea behind the paleo way of eating is that you’re focusing on foods our early ancestors – the hunters and gatherers – would have eaten. Eating according to the paleo diet is commonly suggested for autoimmune conditions, obesity, and blood sugar imbalances – or just for general good health.

On the paleo diet plan, you can eat nuts and seed, healthy fats and animal protein, fruits, vegetables, and some natural sweeteners. What you have to stay away from are dairy products, grains, anything processed (including refined sugars), beans and legumes.


The Keto diet focuses on low carbs and high fat. The addition of (healthy) fats sends your body into ketosis, which means your body is getting its energy by burning fat.

This diet has been used since the 1920s, first to treat epilepsy, then expanded to help with cardiovascular health, diabetes, some types of cancer, brain disorders, and weight loss. Because carbs (which convert to sugar) are limited, the keto diet can really help balance blood sugar levels, helping to avoid issues with insulin resistance.

When eating the keto way, you can eat all non-starchy, low carb vegetables, animal proteins, avocado, coconut, nuts and seeds, and other healthy fats. You’ll avoid all grains, alcohol, sugars, and starchy vegetables such as carrots, sweet potatoes, beets and winter squash, and many fruits.

There are some lower carbohydrate fruits that are allowed (blackberries, raspberries, cantaloupe and watermelon, to name a few) so you’ll have to do some research if this is the route you choose.


The primary focus of the autoimmune protocol is balancing gut dysbiosis and decreasing systemic inflammation.

AIP focuses on eliminating the food chemicals believed to impact these conditions so your body has a chance to recover. While quite similar to paleo style eating, AIP is even more restrictive, especially during the initial elimination phase. Once that’s over, careful reintroduction of foods helps you find the things you can add back in and still feel great.

AIP allows many vegetables, fruits, animal proteins and healthy fats. In the elimination stage, you must cut out grains, beans, legumes, dairy, sugar, nuts and seed, coffee, eggs, chocolate, nightshades, and some seed-based spices. Comprehensive lists are available online to help you know exactly what you can (and cannot) eat in the AIP elimination phase.

So how do you choose the right plan for you? I always suggest working with a qualified professional who can look at all the factors and help guide you towards the right solution for you. There are so many pieces to the puzzle, it may be tough to sort them out on your own. Some of the things to consider before choosing include:

  • Current health status and symptoms
  • Ability to commit to a specific diet for a particular length of time to determine if it’s effective for your problems
  • Time considerations (for shopping, prep work, and cooking)
  • Affordability
  • Lifestyle – what works for you?
  • Cultural expectations and your own personal beliefs

Does the Autoimmune Protocol Diet Help with Hormonal Imbalances?

I have long said that food is the best medicine we have.

AIP, Paleo and Keto all have one thing in common: they focus on healthy, whole foods rather than processed junk. Your body relies on a steady influx of minerals and nutrients to keep things functioning as they should. If something interferes, symptoms appear.

Your hormones are integral to good health. These hormones are how different systems in the body communicate with each other. If that communication goes awry, internal chaos can be the result.

Every one of your major body functions – reproduction, blood pressure, energy levels, metabolism, sleep, appetite, blood sugar balance, and the aging process – are influenced by hormones. That’s why when hormones are imbalanced, you’re likely to notice!

Headaches, fatigue, digestive problems, sleep issues, depression and anxiety, weight gain — the list of symptoms caused by hormonal imbalances goes on and on. Hormones are also connected to inflammation, and with autoimmune disease, inflammation is often behind the pain you feel.

AIP focuses on the gut because a leaky gut can quickly throw hormonal balance off.

With a healthy digestive system, your body will eliminate estrogen metabolites. But if something isn’t right, this may not happen. This can lead to estrogen dominance. Gut health also impacts the conversion of the thyroid hormone T4 to the more usable form T3.

An unhealthy GI tract can also impact both blood sugar and insulin levels, putting you at risk for insulin resistance. And inflammation in your gut can trigger your stress response, leading to high levels of cortisol.

All of this underlines the idea that your hormones can be seriously impacted by what you eat.

The good news is that when you understand that, you realize you have more control than you may have thought! You don’t have to default to medications that may have side effects that are as bad at the symptoms you’re trying to control!

With AIP (or another intentional eating plan) you can discover how certain foods impact your body to help you make informed choices about what you eat.

Incorporating AIP, Paleo or Keto into your life

Changing the way you eat can be overwhelming, especially if you’ve relied on convenience foods and vending machines for far too long. But I can assure you, it’s worth it in the long run – especially if you have an autoimmune disease!

Learning to eat nutritious whole foods in place of processed junk just might be the key to getting back to your favorite activities instead of letting chronic pain and exhaustion run your life!

Here are some tips to help you get started.

Eliminate temptation

In the elimination phase, it’s best to clear your kitchen of anything that’s not allowed. If the things you aren’t supposed to eat aren’t easily available, it’s much easier to convince yourself to grab a healthy snack instead of crackers or cookies.

Prep work can make all the difference

Choose a specific day of the week that you have time available both to shop for fresh ingredients and then prep them so they’re ready when you need them. This one step can make the difference between whipping up a simple but delicious and nutritious stir fry for dinner and ordering takeout.

Deal with the emotions

It’s amazing how often women tell me that starting a restricted eating plan leaves them wanting to eat constantly – even when they know they aren’t hungry. Something about that feeling of being “deprived” leads to seeking out more and more food – and the choices available may seem less than satisfying.

If you find yourself in this situation, take a few minutes to tune into what’s really going on. What feelings are coming up for you when you can’t reach for your favorite “comfort food”? Addressing these will help you be successful in your quest for better health.


Water is so important for health. And often, thirst is mistaken for hunger. You can even use the need for hydration to stave off cravings for sweets – try infusing your water with some berries for a hint of natural sweetness.

Have fun with spices

This is a perfect time to test out some new spice blends to add flavor and excitement to your dishes.

Slow down

Eat slowly and take time to enjoy all the new flavors you may be experiencing. Start training your brain to recognize how delicious whole foods can be by savoring each bite.

Don’t fall into a rut

Though these diets seem quite restrictive, in truth the options are endless. If you stick to fruits and vegetables you already know, or eat the same meals over and over again, you may quickly get tired of them. Branch out and try new recipes. Vary the sides you serve often.

Try new ways of cooking

I love how easy an air fryer makes preparing meats and vegetables, and it’s much quicker than roasting in the oven!

Plan ahead

When eating out, study the menu ahead of time whenever possible. This will help you make choices that stick to your plan instead of ordering on impulse.

Eat well and feel great with an autoimmune/paleo diet

Anything new takes some getting used to. But eliminating foods that can be disrupting your digestive system, throwing hormones out of balance, and causing systemic inflammation can make a huge difference in your life.

Lily gave it a try and discovered that, for her, dairy and gluten needed to stay permanently out of her kitchen. She couldn’t believe how much better she felt when she’d identified these two major culprits! Her pain was so slight and energy so high that she had no problems at all on the hiking vacation she took with her family.

She finally had her life back – and so can you!

Reviewed by Dr. Mark Menolascino, MD