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The Best Autoimmune-Friendly AIP Pizza Recipe

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What if there was a pizza recipe without inflammatory ingredients? I firmly believe everyone deserves to enjoy a slice of pizza. Luckily, with this AIP pizza recipe, you can!

aip pizza recipe

Reading Time: 5 minutes

An AIP pizza recipe is something I’ve been working on perfecting for a long time…

There’s nothing quite like a Friday night at home with a homemade pizza, movie, and glass of red wine. Being from New Jersey, I grew up with Friday night pizza nights on the regular. Pizza was practically its own food group. Unfortunately, knowing what I know now, traditional pizza recipes are filled with inflammatory ingredients— most of which work against our health. In the case of autoimmunity, indulging in pizza is typically a recipe for flare-ups and regrets.

However, what if there was a pizza recipe without those inflammatory ingredients? One of the most frequent requests I get is just that— an AIP pizza recipe. Apparently, I’m not the only one who loves indulging in a hot and fresh slice of pizza every once in a while! It’s definitely the #1 food that people express they miss the most. I can’t tell you how many clients ask for it. And for good reason… pizza is a staple in so many homes growing up. Here’s the deal, I firmly believe everyone (yes, even those with autoimmune disease) deserves to enjoy a slice of pizza. Luckily, with this autoimmune friendly recipe, you can!


Most traditional pizzas are packed with highly inflammatory ingredients. Chances are, whether you have autoimmunity or not, you’ll experience the negative effects of pizza night. Think bloating, gassiness, breakouts, nausea, lethargy, headaches, and more. Gluten, dairy, and preservatives are all common food sensitivities, known to increase overall inflammation, trigger autoimmunity, and negatively impact gut health. 

Inflammatory symptoms typically caused by pizza

This why traditional pizza often leaves you feeling less than optimal:


Traditional pizza crust is made with gluten, which is inflammatory to the gut. Consuming gluten increases the production of zonulin, a protein responsible for loosening junctions in the gut lining. The result? Leaky gut syndrome. Even if you don’t have Celiac disease, it’s likely you could have non-celiac gluten sensitivity (NCGS), especially if you struggle with an autoimmune condition. It’s important to note that many other foods, even some gluten free grains, are cross-contaminated with gluten. This is an important trigger to pay attention to if you have an autoimmune condition.  Needless to say, it’s a big no-no in the case of autoimmunity and gut health. For this reason alone, pizza can create major issues for many people.


Ooey gooey, melted cheese is also a major part of delicious pizza. However, processed and pasteurized dairy, including cheese, increases inflammation and mucus production within the body. You digest conventional dairy, specifically A1 casein dairy (a protein in dairy products), in the small intestine. A1 dairy is often the cause of stomach upset, especially if you have an autoimmune condition. Your body likely doesn’t have the enzyme to properly process and break down this protein, regardless if it’s organic or lactose-free. I recommend most people with autoimmunity and gut issues to avoid conventional dairy products.


Frozen pizzas, pizzas from restaurant chains, and even many homemade pizza recipes are often filled with preservatives, GMO ingredients, and other additives. These are particularly irritating to the gut and can contribute to inflammation and trigger symptoms. It’s no wonder we feel yucky after enjoying a piece of pizza!


My homemade, autoimmune-friendly AIP pizza is a healthy and delicious alternative to traditional pizza. It’s gluten and dairy free, which naturally omits many of the inflammatory ingredients typically found in pizza. In fact, many of these ingredients actually benefit your gut health and reduce autoimmune symptoms:

Gut and autoimmune friendly AIP pizza ingredients
Flax Seed

Flax seed is rich in omega-3 fatty acids, which improves digestion, lowers cholesterol, regulates blood sugar, and reduces inflammation.

Psyllium Husk 

Psyllium husk is a great source of fiber and prebiotics. Similar to flax seed, it can relieve constipation, improve heart health, and regulate blood sugar.

Extra Virgin Olive Oil

We have been using extra virgin olive oil (EVOO) for thousands of years in cooking and homeopathic remedies. It fights oxidative damage, reduces inflammation, and supports brain function.

Gluten Free Flour

Arrow Head Mills Gluten Free All Purpose Flour  is my flour of choice because it is free of corn, which can often trigger inflammation. It also serves as a great alternative to regular all purpose flour!

Dairy Free Pesto 

There are many anti-inflammatory and nutritious ingredients in dairy-free pesto like basil, garlic, and pine nuts. Bonus: garlic naturally has powerful anti-fungal, anti-viral, and antibacterial properties.


There are many autoimmune friendly, anti-inflammatory AIP pizza toppings to choose from! A handful of my favorites are: fresh tomatoes, sun dried tomatoes, artichokes, black olives, basil, red onion, bell pepper, mushrooms, nitrate-free salami, roasted chicken, or fresh garlic.

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The Best Autoimmune Friendly Pizza Recipe

  • Author: Nikki Yelton
  • Total Time: 1 hr 30 mins
  • Yield: 8 servings


This Vegan Pesto Pizza Recipe is loaded with good-for-you ingredients and helps support a healthy gut, body, and mind.


2 ½ cups Gluten Free All Purpose Flour

¼ cup Ground Flaxseed

1 ½ tbs Psyllium Husk Powder

1 tsp Baking Powder

1 tsp Sea Salt

½ tsp Instant Yeast

1 ½ cups Warm Water

½ cup Extra Virgin Olive Oil (plus more for greasing)

½ cup Dairy Free Pesto

Toppings of choice


  1. In a mixing bowl, combine flaxseed, psyllium husk, baking powder, salt, and yeast.

  2. Add the warm water and oil. Mix with a fork, then knead with your hands and form a ball. The dough should be a bit sticky, but hold it’s shape. If too wet, add more psyllium husk. If too dry, add water. Cover with a damp towel and let sit at room temperature for 60 minutes.

  3. Adjust the oven racks to the top and preheat the oven to 500 F. Place a pizza stone or baking sheet in the oven.

  4. Grease your fingers with a bit of olive oil. Transfer the dough to a piece of aluminum foil and gently press into a thin, round layer, roughly ¼” thick. Transfer into the preheating stone or sheet and bake for 8 to 10 minutes.

  5. Spread the pesto evenly over the pizza and top with toppings. Bake for an additional 7 to 9 minutes. Let cool slightly and enjoy!


You can refrigerate this pizza for up to 7 days in an airtight container or freeze it for up to 3 months. We all know pizza is amazing even when reheated! 

Keywords: autoimmune friendly pizza, gut healthy pizza, vegan pizza recipe, healthy pizza recipe, pizza recipe for autoimmunity, pizza recipe for gut health


The foods we eat impact autoimmune disease and gut health. However, that doesn’t mean food can’t still be delicious and enjoyable! Luckily, with a few tweaks, pizza can be a part of any healthy, anti-inflammatory diet. The key is using the freshest, whole food ingredients that support a healthy body!

In this community we like to frame our perspective to see that we don’t have to say no to the things we love, we’re simply saying yes to healing alternatives and a healthy & joyful life! This is why I am ALL about coming up with yummy alternatives to classic faves. There are so many healthy, autoimmune-friendly alternatives to common inflammatory foods. And it just so happens that one of my favorite things to do is help individuals take the stress out of what to eat!

To help you conquer the art of autoimmune-friendly nutrition, I created a customizable Monthly Meal Plan Subscription. The meal plan provides many gut and autoimmune friendly recipes using some of these favorite alternatives. Learn more about this effortless approach to autoimmunity nutrition, here!

The best autoimmune friendly AIP pizza recipe
  1. Sean Molzer says:

    I love this idea and I am just starting my low inflam diet, but how can you list tomato as this is one of the worst inflam foods there is ?

    • Nikki Yelton says:

      I am really happy to hear you are diving into this!! Great question! Tomatoes CAN be inflammatory for some in the earlier stages of healing. I find most do well with tomatoes once their gut is healed and they have reversed autoimmunity/kept it in remission. Eating tomatoes (good quality) won’t CAUSE inflammation, but it can make it worse in those experiencing pain/inflammation and imbalances in the body. I typically suggest listening to your body and see how you respond with or without them. Just because they may not work now though doesn’t mean they can’t be brought back in later. I find this is also the case for potatoes. Moderation is always key of course!!

    • Nikki Yelton says:

      I also want to add that if you are currently in more of an inflammatory state and healing, a homemade pesto would be a great option instead. I’ve even completely omitted tomato sauce and make a bunch of grilled veggies and add that to the pizza with olive oil, arugula, and a balsamic glaze. There are a lot of varieties you can try! I’ve even made a tomato free sauce recipe with carrots. There’s a lot of alternatives out there if you are one of the people who may need to avoid tomato a bit longer.

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"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

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