Autoimmune Keto Diet
Last reviewed: July 23, 2026Last updated: July 23, 2026

Written by: Jay Hastings, CEO of PlexusDx

Jay Hastings is the CEO of PlexusDx, a precision health company focused on genetic testing, blood biomarker insights, and personalized wellness recommendations. He has more than 20 years of experience across healthcare innovation, genomics, laboratory operations, healthcare investing, and strategic finance.

Medically reviewed by: Jayden Lee, PharmD, EMBA

Jayden Lee, PharmD, EMBA, is the PlexusDx Medical Science Liaison with a PharmD and MBA specializing in pharmacogenomics and clinical product development. Dr. Lee has more than 10 years of professional experience in clinical pharmacy, academia, and research.

Autoimmune Keto Diet

The Autoimmune Keto Diet combines the principles of an autoimmune protocol with a ketogenic approach to lower inflammation and support immune balance. By restricting carbohydrates to under 25 grams of net carbs daily, this plan minimizes blood sugar fluctuations while simultaneously removing common immune triggers found in standard diets. This specialized meal plan is designed to be gluten-free, grain-free, dairy-free, and egg-free, ensuring that you adhere to a strict elimination phase that avoids nightshades, legumes, nuts, and seeds. This approach is particularly relevant if your PlexusDx report identifies variations in inflammation-regulating genes like TNF, IL6, and CRP, which control how your body signals and resolves inflammatory responses. Additionally, because the diet emphasizes nutrient-dense, low-toxin foods, it supports pathways related to gut defense and detoxification, relevant to genes such as IL23R and ABCC2.

This program is built on evidence suggesting that specific dietary strategies can modulate immune function and reduce oxidative stress. The plan prioritizes polyphenols and fiber to manage C-reactive protein levels, prebiotics to restore the gut barrier, and essential fats to support hormone regulation and liver health. To help you implement these science-backed principles, we have curated a list of key dietary focus areas:

  • Consume Anti-Inflammatory Vegetables: Incorporate spinach and olives to provide polyphenols that help control oxidative stress and modulate the inflammatory response.
  • Support Gut Health: Eat asparagus, garlic, and leafy greens to provide prebiotic fiber that feeds beneficial bacteria and restores the gut barrier.
  • Boost Liver Function: Include cruciferous vegetables like broccoli, cauliflower, and kale, which contain indoles (like indole-3-Carbinol) essential for liver detoxification and hormone balance.
  • Prioritize Omega-3 Fats: Obtain healthy fats from salmon, mackerel, and sardines to assist with cortisol regulation and reduce inflammation.
  • Enhance Immune Defense: Ensure adequate intake of zinc and selenium from meats and poultry, and Vitamin A and C from nutrient-dense produce like lemon, kale, and spinach to support antioxidant status.

To start following this plan, click the button below to access your personalized PlexusDx meal planning tool. If you need to adjust any meals to better fit your preferences or inventory, you can easily find alternatives that adhere to the autoimmune and ketogenic rules using our "Swap" feature. Follow these simple steps to customize your menu:

  1. Locate the meal you wish to change on your daily planner.
  2. Click the three dots next to the meal name.
  3. Select "Swap recipe" from the menu options.
  4. Choose "Swap" to change a single meal or "Swap all" to replace that recipe for the entire week.
  5. Keep clicking "Swap" to browse through alternatives that match your specific plan rules, such as gluten-free, dairy-free, and egg-free options.

PlexusDx provides educational information about genetic predispositions only. This content is not medical advice. Always discuss genetic findings, test results, symptoms, and treatment decisions with your healthcare provider or an allergist to determine appropriate care for your situation.


Frequently Asked Questions About The Autoimmune Keto Diet

What is the Autoimmune Keto Diet and who is it designed for?

The Autoimmune Keto Diet combines an autoimmune protocol with a ketogenic approach to lower inflammation and support immune balance. It keeps carbs under 25 grams of net carbs daily to minimize blood sugar fluctuations and uses a strict elimination phase that is gluten-free, grain-free, dairy-free, and egg-free. It’s especially relevant if your PlexusDx report flags inflammation-regulating genes such as TNF, IL6, and CRP, along with gut-defense and detox pathways involving IL23R and ABCC2.

What foods and nutrients does the Autoimmune Keto Diet focus on?

The plan prioritizes nutrient-dense, low-toxin foods and targets inflammation and oxidative stress using polyphenols and fiber, plus prebiotics to support the gut barrier. It emphasizes anti-inflammatory vegetables (like spinach and olives), gut-support foods (asparagus, garlic, leafy greens), liver-support cruciferous vegetables (broccoli, cauliflower, kale), omega-3 fats from salmon, mackerel, and sardines, and immune/antioxidant support through nutrient-dense produce and minerals such as zinc and selenium.

How can I customize meal plans while staying gluten-free, dairy-free, and egg-free?

You can use the PlexusDx personalized meal planning tool to customize your menu with the “Swap” feature. Start by selecting the meal you want to change on your daily planner, click the three dots next to the meal name, choose “Swap recipe,” then pick “Swap” for a single meal or “Swap all” to replace the recipe for the entire week. Continue swapping until you find alternatives that follow the autoimmune and ketogenic rules, including gluten-free, dairy-free, and egg-free options.

What tests can help me learn more about Autoimmune Keto Diet?

The Functional Health Genetic Test delivers over 750 personalized genetic insights across 10 in-depth genetic reports to support whole-body, systems-level health understanding. The Diet and Nutrition Genetic Report translates your results into personalized, actionable guidance. Your healthcare provider can also recommend targeted blood tests based on your specific pathway results and health history to complement your genetic insights with current biomarker data.


Medical and Editorial Standards

Medical review process: This article was reviewed for medical accuracy, scientific clarity, evidence alignment, and appropriate discussion of nutrition, genetics, biomarkers, and health-related claims.

Sources and evidence: PlexusDx educational content is developed using peer-reviewed research, clinical literature, and reputable medical references.

Important disclaimer: This content is for informational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always consult a qualified healthcare provider before making decisions about your diet, supplements, or health-related care.