Avoiding Paleo Pitfalls: Fibers You Must Include on AIP

An Autoimmune Paleo (AIP) diet can be great for reducing inflammation, improving immune function, boosting energy, and enhancing quality of life (1,2,3). However, if you’re not including certain key foods, these diets can backfire—leading to digestive issues, fatigue, poor mental health, and even weight gain (4,5).

At first, these issues may not surface, but prolonged adherence to AIP without specific nutrients (keep reading for details) increases the risk of many adverse health effects (4,5).

KEY CONCEPT: 

Fibers and polyphenols—naturally occurring plant compounds—are essential for feeding beneficial gut bacteria. We have thousands of bacterial species that live in our gut! 

Each type of fiber feeds different bacterial species, and research has discovered that the diversity of microbial species is one of the main drivers of our health (4,5,6)!

These microbes influence everything from digestion and metabolism to immune function and hormone balance.

The Fiber Mistake That Can Wreck Your AIP Diet

There are critical fibers and polyphenols found in foods excluded on AIP—such as seeds, nuts, grains, and legumes—that literally feed your beneficial gut bacteria (1,2,3). And trust me, you want those little guys thriving!

You may have heard of soluble and insoluble fiber, but did you know there are actually dozens of fiber types like soluble gums, resistant starch, and galactooligosaccharides (6)?

Nuts, seeds, grains, and legumes are rich in these unsung fiber heroes. Since each fiber type plays a unique and crucial role in gut health, it’s essential to eat a variety of plant-based foods (1,2).

But wait—what about the argument that "humans didn’t evolve to eat grains and legumes", as they were introduced relatively recently in the grand scheme of human existence? That’s a valid point! Skeletal records suggest a decline in bone health after the agricultural revolution (7). Check our other blog post where we dive into this topic to try to make sense of it all.

The good news? There’s a way to do AIP the right way and get the fiber your gut microbiome needs!

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AIP-Friendly Fiber Swaps You Need to Know

Here are the key fibers and prebiotics missing from AIP diets—and the best AIP-friendly alternatives to keep your gut healthy:

🔹 Soluble Gum Fibers – Typically in almonds and chia seeds. AIP-friendly sources: okra, aloe vera, certain squashes (9).
✔ Try: Paleo On the Go Smoked Salmon Breakfast Bowl (contains butternut squash).

🔹 Resistant Starch – Found in oats, legumes, and rice. AIP-friendly sources: plantains, sweet potatoes (must be cooked & cooled), green-tinted bananas (10).

Resistant starch plays a vital role in gut health by promoting the production of short-chain fatty acids (SCFAs) like butyrate, which helps maintain a healthy gut lining, reduce inflammation, and support metabolic health.

Note: Different types of resistant starch exist, with Type 1 being primarily found in seeds and grains—foods excluded on AIP. This highlights the importance of a reintroduction phase to restore gut microbial balance and access the full spectrum of fiber benefits.

✔ Try: Paleo On The Go Loaded Baked Sweet Potato Soup or Beef Chimichurri with Roasted White Sweet Potatoes.

🔹 Beta-Glucans – Known for boosting the immune system, these fibers are found in oats and barley. AIP-friendly source: mushrooms (11).

Beta-glucans are crucial for immune regulation, cholesterol balance, and gut health. Research highlights their role in modulating immune function, reducing inflammation, and supporting a healthy microbiome. Regular intake of beta-glucan-rich foods, like mushrooms, may enhance gut barrier integrity and contribute to overall metabolic health (11).

✔ Try: Paleo On The Go Beef Bourguignon (contains mushrooms).

🔹 GOS Fibers – Mainly in legumes. AIP-friendly sources: artichokes, asparagus, dandelion greens (12).

GOS fibers are like fuel for good gut bacteria that help to balance blood sugar, improve cholesterol levels, and support a healthy weight. For those with autoimmunity, this is key—stable blood sugar and a well-functioning metabolism can help keep inflammation in check and support overall immune balance. Adding GOS-rich foods to your diet may be a simple way to improve both gut and metabolic health (12).

🔹 Lignans – Found in flaxseeds, legumes, and whole grains. AIP-friendly sources: cruciferous veggies (broccoli, kale, cabbage, Brussels sprouts), garlic, apricots (8).

Lignans are polyphenols that act as prebiotics, supporting gut bacteria and can do wonders for balancing hormones (especially estrogen!) and immune function (8).

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How to Put This Into Practice

Once your immune system calms down and your health improves, it’s critical to begin a reintroduction phase to expand your diet.

✅ My approach:
I start my autoimmune clients with a strict 6-week AIP protocol, then strategically reintroduce small amounts of the following to see which are tolerated:
✔ Seeds
✔ Nuts
✔ Gluten-free ancient grains
✔ Pre-soaked, pressure-cooked legumes

How do I decide what to reintroduce first? I use lab testing + symptom tracking to personalize the process.

Long-term success for those with an autoimmune condition usually looks like this: Use the AIP diet as your base, with your safe reintroduction foods sprinkled in. This approach has been highly successful for my clients!

🚨 Bloating with certain fibers? This could indicate bacterial or fungal overgrowths—you may need to work with a practitioner to restore gut balance first.

Did this info trigger more questions for you, or is there another topic you’d like to hear more about?  >> Submit your request to this form on my website <<

References: 

1. Pardali EC, Gkouvi A, Gkouskou KK, et al. Autoimmune protocol diet: A personalized elimination diet for patients with autoimmune diseases. Metabol Open. 2024;25:100342. Published 2024 Dec 30. doi:10.1016/j.metop.2024.100342

2. Abbott RD, Sadowski A, Alt AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis. Cureus. 2019;11(4):e4556. Published 2019 Apr 27. doi:10.7759/cureus.4556

3. Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221

4. Leeming ER, Johnson AJ, Spector TD, Le Roy CI. Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration. Nutrients. 2019;11(12):2862. Published 2019 Nov 22. doi:10.3390/nu11122862

5. Grace-Farfaglia P, Frazier H, Iversen MD. Essential Factors for a Healthy Microbiome: A Scoping Review. Int J Environ Res Public Health. 2022;19(14):8361. Published 2022 Jul 8. doi:10.3390/ijerph19148361

6. Cronin P, Joyce SA, O'Toole PW, O'Connor EM. Dietary Fibre Modulates the Gut Microbiota. Nutrients. 2021;13(5):1655. Published 2021 May 13. doi:10.3390/nu13051655

7. Mummert A, Esche E, Robinson J, Armelagos GJ. Stature and robusticity during the agricultural transition: evidence from the bioarchaeological record. Econ Hum Biol. 2011;9(3):284-301. doi:10.1016/j.ehb.2011.03.004

8. Álvarez-Caballero JM, Coy-Barrera E. Lignan. In: Antioxidants Effects in Health. 2022. ScienceDirect. Accessed March 1, 2025. https://www.sciencedirect.com/topics/nursing-and-health-professions/lignan

9. BeMiller J, Whistler R, Chen CC. Aloe, chia, flaxseed, okra, psyllium seed, quince seed, and tamarind gums. Materials Science, Agricultural and Food Sciences. 1993.

10. Patterson MA, Maiya M, Stewart ML. Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review. J Acad Nutr Diet. 2020;120(2):230-244. doi:10.1016/j.jand.2019.10.019

11. Cerletti C, Esposito S, Iacoviello L. Edible Mushrooms and Beta-Glucans: Impact on Human Health. Nutrients. 2021;13(7):2195. Published 2021 Jun 25. doi:10.3390/nu13072195

12. Kaur AP, Bhardwaj S, Dhanjal DS, et al. Plant Prebiotics and Their Role in the Amelioration of Diseases. Biomolecules. 2021;11(3):440. Published 2021 Mar 16. doi:10.3390/biom11030440