An Autoimmune Protocol (AIP) Guide: What Cheese Is AIP and How to Find Dairy-Free Alternatives

October 28, 2025 •

4 min read

The Autoimmune Protocol (AIP) is an elimination diet designed to help manage inflammation and symptoms for those with autoimmune conditions, and it requires the removal of dairy during the initial phase. For those adhering to this diet, understanding what cheese is AIP is crucial, and the short answer is that no traditional cheese from cow's or goat's milk is permitted. This necessitates turning to creative, dairy-free alternatives to achieve that desired cheesy flavor and texture.

Quick Summary

Traditional cheese is eliminated during the AIP's initial phase due to its inflammatory potential, meaning no conventional cheese is AIP-compliant. However, safe and tasty alternatives can be created at home using ingredients like nutritional yeast and coconut milk, while dairy products can be systematically reintroduced in later stages.

Key Points

Dairy Is Not AIP: Conventional cheese and all other dairy products must be eliminated during the Autoimmune Protocol's initial phase.
AIP "Cheeze" is Homemade: Store-bought vegan cheeses often contain non-compliant ingredients, so the best AIP cheese alternatives are made at home from approved ingredients.
Nutritional Yeast Provides Cheesy Flavor: A key ingredient for recreating a savory, cheesy taste is unfortified nutritional yeast.
Coconut Milk Creates Creaminess: Full-fat coconut milk or cream is the ideal base for achieving a creamy texture in AIP cheese sauces and blocks.
Tapioca Starch Adds Stretch: For a meltable and stretchy consistency reminiscent of mozzarella, tapioca starch is a crucial component in AIP cheese recipes.
Ghee is the First Dairy Reintroduction: Dairy reintroduction on AIP follows a strict protocol, beginning with clarified butter (ghee) before attempting more complex dairy products like cheese.
Reintroduction is a Personal Process: The reintroduction of foods like cheese is a systematic, individual-based process to test for personal tolerance and identify which foods, if any, can be added back into the diet.

Understanding the Elimination Phase and Dairy Restriction

In the Autoimmune Protocol, dairy is one of the key food groups that is strictly eliminated. This is because dairy, particularly cow's milk products, contains proteins like casein and lactose that can potentially trigger an inflammatory response or cause gut permeability (often referred to as 'leaky gut') in some individuals with autoimmune conditions. The goal of the AIP elimination phase, which typically lasts from 30 to 90 days, is to remove these potential triggers to allow the gut to heal and inflammation to subside.

During this time, the body's immune system can calm down, and symptoms related to the autoimmune disease can improve. This means any product derived from milk, including cheese, yogurt, and butter (with the exception of ghee, which is often a later reintroduction), is off the menu. While this may seem daunting, especially for cheese lovers, the good news is that many delicious and flavorful alternatives can fill the void.

Creating Satisfying AIP-Compliant "Cheeze" Alternatives

Since store-bought vegan cheeses often contain non-AIP ingredients like nuts, seeds, and additives, the best approach is to make your own at home. By using a combination of AIP-friendly ingredients, you can replicate the creamy, salty, and savory experience of traditional cheese.

Key Ingredients for AIP "Cheeze"

Nutritional Yeast: This is the secret weapon for a cheesy flavor profile. It is a deactivated yeast grown on molasses, is gluten-free, and imparts a distinct savory, umami taste without being an inflammatory trigger for most. Be sure to use an unfortified variety, as many fortified versions contain synthetic vitamins that are not AIP-compliant.
Coconut Milk or Cream: This forms the creamy, rich base for most AIP cheeses and sauces. Full-fat coconut milk or the cream scooped from the top of a chilled can works best for a dense, creamy texture. Some recipes may call for coconut butter as well.
Tapioca Starch or Flour: This is essential for achieving a stretchy, meltable texture similar to mozzarella. When heated with coconut milk, tapioca starch creates a gooey, pliable consistency that works wonderfully for pizza or nachos.
Flavor Boosters: A tang of apple cider vinegar or lemon juice can mimic the acidity found in aged cheeses. A high-quality AIP-compliant fat, such as lard or extra-virgin olive oil, can add depth of flavor.
Sea Salt: A must-have for bringing out all the flavors and providing that salty contrast.

Examples of AIP Cheese Recipes

Meltable Mozzarella: Using coconut milk, tapioca starch, nutritional yeast, and gelatin, you can create a sliceable, meltable mozzarella alternative that works perfectly on AIP pizza or lasagna.
Creamy Nacho Sauce: A smooth, savory sauce can be made by blending cooked sweet potato or squash with nutritional yeast, coconut milk, and spices.
Savory Zucchini Cheese: Some recipes use boiled and blended zucchini as a base for a versatile, allergen-free cheese sauce.
Parmesan-Style Topping: For a hard, crumbly texture, a dairy-free parmesan can be made from nutritional yeast, coconut oil, coconut butter, and a bit of turmeric for color.

The Dairy Reintroduction Phase

Following a period of strict elimination, the AIP protocol progresses to a reintroduction phase where foods are tested individually to identify personal triggers. When it comes to dairy, there is a specific order to follow, starting with the least allergenic forms. This process is gradual and requires careful monitoring for any adverse reactions.

A typical dairy reintroduction schedule might include:

Ghee: Clarified butter, with its casein and lactose removed, is often the first dairy product to be tested. It is introduced in small amounts and monitored for several days.
Butter: If ghee is tolerated, the next step may be reintroducing high-quality, grass-fed butter.
Fermented Dairy: Products like kefir and yogurt, which are fermented and lower in lactose, can be introduced next.
Hard Cheeses: Some types of hard cheeses aged for at least six months, which naturally contain less lactose and casein, can be a later reintroduction.
Soft Cheeses and Milk: Finally, softer cheeses and milk are reintroduced, as they have the highest concentrations of potentially problematic proteins.

Comparison of Traditional Cheese and AIP Alternatives


Feature	Traditional Dairy Cheese	Homemade AIP "Cheeze" Alternatives
Primary Ingredients	Cow's milk, goat's milk, or sheep's milk, rennet, enzymes	Coconut milk/cream, tapioca starch, nutritional yeast, gelatin
AIP Elimination Status	Not AIP-compliant during elimination phase	AIP-compliant using allowed ingredients
Potential Inflammatory Triggers	Contains casein and lactose, which can be inflammatory for some individuals	Free of common dairy-related inflammatory triggers
Texture	Varies widely from soft and creamy to hard and crumbly	Can be formulated to be creamy, gooey, or hard, depending on ingredients
Flavor	Rich, complex, and savory, depending on age and type	Savory and cheesy due to nutritional yeast and other flavorings
Reintroduction Protocol	Introduced gradually and late in the reintroduction phases	Safe for consumption throughout the AIP elimination phase
Best For	Used in countless recipes and dishes	Ideal for recreating cheesy sauces, melting toppings, and savory spreads

Conclusion

For those on the Autoimmune Protocol, the question of what cheese is AIP is an important one. The answer is that no traditional dairy cheese is compliant during the strict elimination phase due to its potential to cause inflammation. However, this dietary restriction does not mean sacrificing delicious, cheesy flavors. By creatively using AIP-compliant ingredients like nutritional yeast, coconut milk, and tapioca starch, you can craft satisfying homemade cheese alternatives that are both flavorful and safe for your diet. With time and careful monitoring, dairy products can eventually be reintroduced in a staged approach, starting with less reactive options like ghee. Adhering to these guidelines allows individuals to enjoy their food while supporting their body's healing process.

For additional guidance on navigating the AIP diet, the Paloma Health website offers comprehensive resources on dairy-free alternatives. Paloma Health

Frequently Asked Questions

Conventional cheese is not allowed on the AIP diet because it contains dairy proteins like casein and lactose, which are common inflammatory triggers and can contribute to gut dysfunction in individuals with autoimmune conditions.

Yes, nutritional yeast is an AIP-compliant ingredient that is widely used to provide a cheesy, savory flavor in recipes. Be sure to source an unfortified version to ensure compliance.

A meltable mozzarella alternative can be made using a combination of full-fat coconut milk, tapioca starch, nutritional yeast, and gelatin. The tapioca starch provides the characteristic stretchy texture.

Ghee is generally not allowed during the initial elimination phase of the AIP diet but is one of the first dairy products to be reintroduced in a later phase. It is a clarified butter with most of the lactose and casein removed.

Hard cheeses are typically among the last dairy products to be reintroduced during the AIP protocol. They are generally tested only after less allergenic dairy items like ghee have been successfully added back into the diet without a reaction.

Most store-bought vegan cheese alternatives contain nuts, seeds, or additives that are not compliant with the AIP diet. It is recommended to make your own cheese substitutes from scratch using AIP-approved ingredients.

Creaminess in AIP cheese substitutes is typically achieved by using full-fat coconut milk or cream, along with starchy vegetables like sweet potatoes or zucchini, and the addition of nutritional yeast for flavor.