Understanding the Rules: Can you have flour on an AIP diet?

October 13, 2025 •

4 min read

Over 70% of your immune system resides in your gut, which is why the Autoimmune Protocol (AIP) focuses on eliminating dietary triggers to promote healing. One of the most common questions for those new to this plan is: Can you have flour on an AIP diet? The simple answer is that while traditional grain-based and seed flours are excluded, several nutrient-dense alternatives are fully compliant.

Quick Summary

Traditional flours made from grains, nuts, and seeds are removed during the AIP elimination phase to reduce gut inflammation. The diet permits specialty flours derived from roots and fruits, such as cassava, coconut, and tigernut, as compliant alternatives for cooking and baking.

Key Points

No Traditional Flours: Flours from grains (wheat, rice, corn) and seeds (almond, sunflower) are excluded during the AIP elimination phase to reduce inflammation.
AIP-Compliant Alternatives: Acceptable flours are derived from roots and tubers, including cassava, tapioca starch, coconut, and tigernut.
Unique Baking Properties: AIP-compliant flours have different textures and absorption rates compared to wheat flour, often requiring a blend of flours for optimal results.
Reintroduction Process: After a period of elimination, certain flours can be reintroduced systematically to test for individual tolerance.
Support Gut Healing: The focus of eliminating potentially irritating flours is to allow the gut lining to heal and improve overall autoimmune symptoms.

The Autoimmune Protocol (AIP) is a diet designed to help manage symptoms of autoimmune diseases by reducing inflammation and healing the gut. It is a stricter version of the Paleo diet, built on the premise that certain foods can trigger an immune response in sensitive individuals. The initial elimination phase requires removing common inflammatory foods, including grains, legumes, nightshades, nuts, seeds, dairy, and eggs. While this may seem daunting, especially for those who rely on baked goods, the AIP diet offers several excellent alternatives to make your transition manageable.

The Elimination Phase: Why Traditional Flours Are Out

During the AIP elimination phase, the objective is to give the body a rest from potential immune triggers and allow the gut lining to repair itself. Traditional flours are banned for several key reasons:

Grains: Flours derived from grains like wheat, rice, corn, and oats are eliminated because they contain compounds such as lectins, phytic acid, and saponins. For individuals with autoimmune issues, these compounds can irritate the gut lining, potentially contributing to 'leaky gut' syndrome. Grains also have a high glycemic index, which can cause blood sugar spikes that trigger inflammation.
Nuts and Seeds: Flours made from nuts (e.g., almond flour) and seeds (e.g., sunflower seed flour) are also excluded. This is because nuts and seeds contain similar compounds like lectins and phytic acid, which can also provoke an immune response in sensitive people. Seed-based spices are also avoided.
Cross-Contamination Concerns: Even certified gluten-free grain flours are avoided initially because the immune system can react to non-gluten proteins or other components in the grains.

The Best AIP-Compliant Flour Alternatives

Fortunately, for those who enjoy baking, the AIP diet is not flour-free. It simply requires switching to specialty flours made from approved root vegetables and fruits. These options provide a nutrient-dense base for creating everything from bread and cookies to crackers and thickeners.

Common AIP Flours

Cassava Flour: Made from the whole peeled and dried cassava root (also known as yuca), this flour is a fantastic, neutral-flavored, and starchy option. Its soft, powdery texture behaves similarly to wheat flour, making it a favorite for doughs, tortillas, and bread.
Tapioca Starch (or Flour): This is a starch extracted from the cassava root. It adds a desired chewiness and lightness to baked goods and is an excellent thickener for sauces and gravies. It is best used in combination with other flours.
Coconut Flour: Produced from dried and ground coconut meat, coconut flour is high in fiber and absorbs a lot of liquid. Due to its high absorbency, it is typically used in smaller quantities and combined with other flours to prevent dryness. It imparts a mild coconut flavor.
Tigernut Flour: Don't be fooled by the name; tigernuts are small tubers, not nuts. Tigernut flour has a slightly sweet, nutty flavor and is rich in prebiotic fiber. It can be used in baked goods to add a lovely crumb and natural sweetness.
Arrowroot Powder: Similar to tapioca starch, arrowroot is a pure starch from the roots of the Maranta arundinacea plant. It works well as a thickener and can add a light texture to baking.
Green Banana Flour: This flour is made from unripe green bananas and can also be used in AIP baking. It is high in resistant starch and has a mild flavor.

AIP-Compliant Flours vs. Non-Compliant Flours


Feature	AIP-Compliant Flours (Cassava, Tigernut)	Non-Compliant Flours (Wheat, Almond)
Source	Tubers, roots, and fruits	Grains, nuts, and seeds
Digestibility	Generally easy to digest; supportive of gut health	Contains anti-nutrients (lectins, phytates) that can irritate the gut
Inflammation	Designed to be non-inflammatory	Potential triggers for inflammation and autoimmune flares
Nutrient Density	Nutrient-dense alternatives, often high in fiber	May be less nutrient-dense, especially refined versions
Baking Properties	Requires specific blending ratios due to high absorbency or starch content	More predictable behavior due to gluten or established baking properties
Reintroduction	Safe for immediate use during elimination phase	Only reintroduced individually and carefully in Phase 2

How to Use AIP Flours for Baking

Baking with AIP flours requires some experimentation, as they lack the binding properties of gluten. A common strategy is to create a blend of different AIP flours to achieve the desired texture.

Blending is Key: Combine a heavy, dense flour like cassava with a lighter starch such as tapioca or arrowroot to achieve a good crumb.
Use Binders: Because eggs are eliminated, binders like gelatin powder or pureed fruit can be used to hold baked goods together. For leavening, a combination of baking soda and a bit of apple cider vinegar works well.
Hydration: Coconut flour is highly absorbent, so recipes using it will require extra liquid. Resting the dough after mixing is also important to allow the flours to absorb the moisture.

The Reintroduction Phase and Expanding Your Flour Options

Once your autoimmune symptoms have subsided (which may take anywhere from 30 to 90 days), you can begin the systematic reintroduction phase.

Test Foods One by One: Reintroduce potential trigger foods, like gluten-free grains or seed-based flours, one at a time.
Monitor Your Reaction: Carefully track any return of symptoms over a 5-day observation period. This helps you identify individual food sensitivities and build a personalized long-term diet.
Keep a Food Journal: Documenting your reintroductions and any subsequent reactions is crucial for success.

Conclusion: Navigating Flour Choices on an AIP Diet

While you cannot have traditional flour on an AIP diet during the elimination phase, you are not without delicious and functional alternatives. By using flours made from tubers and fruits like cassava, coconut, and tigernut, you can still enjoy a wide variety of foods while supporting your body's healing process. The protocol is not about permanent deprivation but about a process of discovery that leads to a more personalized and sustainable way of eating for long-term wellness. Focusing on nutrient density and gut repair with AIP-compliant flours helps pave the way for a successful reintroduction phase and a thriving, symptom-reduced life.

Autoimmune Wellness: Your Comprehensive Guide to the AIP Diet

Frequently Asked Questions

Grains are eliminated on the AIP diet because they contain compounds like lectins and phytates that can irritate the gut lining and potentially trigger an immune response. Even gluten-free grains can contain these compounds, and the elimination phase is designed to remove all such potential irritants to promote gut healing.

Cassava flour is a grain-free flour made from the whole, peeled, and dried cassava root. It is a compliant, starchy flour used widely in AIP baking because it performs most similarly to wheat flour.

No, almond flour is not allowed during the AIP elimination phase. The protocol excludes all nuts and seeds, as they contain compounds that can cause gut irritation for sensitive individuals.

Coconut flour is very absorbent, so recipes using it require more liquid than conventional flours. It is often used in combination with other AIP-compliant flours to achieve a better texture and prevent baked goods from becoming too dry.

No, while both come from the cassava root, they are different. Cassava flour is made from the whole root, whereas tapioca starch is the isolated starch. They cannot be used interchangeably in all recipes.

To replace eggs in AIP baking, you can use binders like gelatin powder, mashed banana, applesauce, or sweet potato puree. The choice depends on the desired texture and flavor profile.

Reintroduction can begin after a minimum of 30 days on the elimination diet, provided your autoimmune symptoms have significantly improved. A slow, systematic process is followed, introducing one food at a time and monitoring for reactions over several days.