And Do You Need to Go Back to AIP Elimination?
If you've been following the Autoimmune Protocol for a while and suddenly experience an autoimmune flare, one question tends to come up almost immediately:
"Do I need to go back to strict AIP?"
The answer may surprise you.
Not necessarily.
One of the greatest strengths of the Autoimmune Protocol is that the elimination phase is meant to be temporary. Its purpose is to reduce your inflammatory burden while helping you identify which foods truly work for your body. Once you've completed thoughtful reintroductions, your diet becomes uniquely yours.
That means if you've successfully reintroduced foods like eggs, white rice, or certain seeds without symptoms, a flare doesn't automatically erase all of that progress.
Instead of asking, "What foods do I need to eliminate?" I encourage asking a different question:
"How can I create the most supportive environment for my body to heal?"
Because while food is incredibly powerful, it's only one piece of the healing puzzle.
Think of Your Body Like a Bank Account
One analogy I often share with clients is to think of your body like a bank account.
Every day, you're either making deposits or withdrawals.
A nourishing meal is a deposit.
A good night's sleep is a deposit.
Time outdoors, laughter, meaningful connection, and moments of rest are all deposits.
On the other hand, chronic stress, poor sleep, infections, environmental toxins, overexercising, emotional overwhelm, and foods that don't agree with you can all become withdrawals.
During an autoimmune flare, your account may already be running low.
Rather than focusing solely on removing foods, your goal becomes making as many deposits as possible while minimizing unnecessary withdrawals.
Healing isn't just about avoiding inflammation.
It's about creating the conditions that allow your body to recover.
Do You Need to Return to Full AIP Elimination?
Not necessarily.
If you've reintroduced foods that consistently make you feel well, there's often no reason to eliminate them simply because you're experiencing a flare.
However, this probably isn't the time to push your boundaries either.
If there are foods you've noticed leave you feeling slightly more inflamed, bloated, congested, or fatigued—even if you occasionally tolerate them—it may be wise to give your body a temporary break while you're recovering.
Think of it as reducing your overall inflammatory load rather than starting over.
This isn't about punishment.
It's about giving your immune system one less thing to manage while it focuses on healing.
A Flare Is Your Body Asking for More Support
One of the biggest lessons I learned on my own healing journey is that our bodies are incredibly intelligent.
A flare isn't necessarily your body failing.
It's often your body communicating that it needs more resources.
More nourishment.
More rest.
More recovery.
Less stress.
Sometimes a flare follows an illness. Other times it comes after weeks of pushing ourselves too hard, traveling, sleeping poorly, navigating emotional stress, or simply forgetting to slow down.
Food may play a role—but it isn't always the root cause.
Instead of responding with fear or restriction, I encourage you to revisit all of the pillars that support healing.
Rest Is Part of the Treatment Plan
Many of us have become experts at pushing through.
We'll cook one more meal.
Answer one more email.
Run one more errand.
Clean the kitchen before sitting down.
But healing asks something different of us.
During an autoimmune flare, one of the most therapeutic things you can do is rest.
If your schedule allows, aim for 9-10 hours of quality sleep each night while you're recovering. Deep sleep is when much of the body's repair work occurs, and giving yourself permission to sleep more is one of the greatest gifts you can give your immune system.
Rest may also look like saying no to commitments, asking for help, spending time in nature, practicing deep breathing, reading a book, or simply allowing yourself an afternoon on the couch without guilt.
Healing isn't lazy.
Healing is productive.
Flood Your Body With Nutrients
Rather than focusing on everything you're removing, shift your attention toward everything you can add.
This is the time to flood your body with nutrient-dense foods that provide the vitamins, minerals, amino acids, antioxidants, and healthy fats your immune system needs to function optimally.
Build your meals around:
- High-quality pasture-raised or grass-fed proteins
- Plenty of colorful cooked vegetables
- Bone broth and collagen-rich foods
- Organ meats if you enjoy them
- Healthy fats like olive oil, avocado, coconut, and grass-fed tallow
- Gentle starches such as sweet potatoes, winter squash, or plantains to help support healthy blood sugar and provide your body with the energy it needs to heal
Think of every meal as another opportunity to make a deposit into your healing account.
Support Your Gut
Approximately 70% of the immune system resides in and around the gut, making digestive health an important part of immune regulation.
During a flare, many people also notice increased digestive symptoms, bloating, or food sensitivities.
This can be a wonderful time to intentionally support your gut with foods that nourish the intestinal lining while helping maintain a healthy microbial balance.
I love incorporating foods and culinary herbs such as:
- Bone broth
- Slow-cooked meats
- Garlic
- Oregano
- Ginger
- Rosemary
Depending on the individual and in collaboration with a qualified healthcare practitioner, targeted botanicals such as berberine may also be appropriate to help support a healthy gut microbiome.
Consider Strategic Supplement Support
Food should always be the foundation, but during times of increased immune activity, strategic supplementation can provide additional support.
One protocol I frequently recommend focuses on what we call the "Fab Five":
- Liquid Vitamin D and other fat-soluble vitamins
- Omega-3 fatty acids
- Liposomal glutathione
- Short-chain fatty acids such as butyrate
- A high-quality probiotic
Together, these nutrients help regulate the immune system, promote gut barrier integrity, and support the function of regulatory T cells—the specialized immune cells responsible for helping keep the immune system balanced.
As with any supplement, always work with your healthcare practitioner to determine what's appropriate for your individual situation.
Keep Meals Gentle and Keep Them Easy
If digestion feels more sensitive than usual, now isn't the time for elaborate recipes or ambitious meal prep.
Instead, lean into meals that are warm, nourishing, and easy to digest.
Think:
- Soups
- Stews
- Slow-cooked meats
- Cooked vegetables
- Bone broth
- One-pan meals
Warm foods often feel more supportive than cold meals or large raw salads when your digestive system is under stress.
But there's another piece that's just as important.
Keep your meals easy.
One thing I wish more people realized is that cooking itself requires energy.
Planning meals.
Driving to the grocery store.
Shopping.
Standing in the kitchen.
Chopping vegetables.
Cooking.
Doing dishes.
Cleaning the kitchen.
When you're in the middle of a flare, all of those tasks become withdrawals from your healing account.
If you've stocked your freezer with nourishing meals ahead of time, now is the perfect time to use them.
If a family member offers to cook for you, say yes.
If nourishing prepared meals allow you to spend that energy resting instead, that's not taking a shortcut.
That's practicing self-care.
Sometimes conserving your energy is just as therapeutic as the food itself.
Hydration Matters Too
Don't forget about hydration.
Water, mineral-rich bone broth, herbal teas, and electrolyte-rich fluids all help support your body's normal healing processes.
Sometimes a warm mug of broth or herbal tea is exactly what your body needs when a full meal feels overwhelming.
Give Yourself Grace
Perhaps the most important reminder of all:
A flare is not a sign that you've failed.
Healing is rarely linear.
There will be seasons where your body asks for more support than others.
Meet those moments with compassion instead of criticism.
Sleep more.
Rest more.
Ask for help.
Let someone else wash the dishes.
Choose the prepared meal instead of cooking from scratch.
Cancel the nonessential plans.
Protect your energy as fiercely as you protect your nutrition.
Because every decision that reduces stress and conserves your energy is another opportunity to support healing.
The Bottom Line
An autoimmune flare doesn't automatically mean you need to return to strict AIP elimination.
If you've successfully reintroduced foods that consistently support your body, there's often no need to remove them. Instead, consider temporarily setting aside foods that may be mildly reactive while shifting your attention toward the bigger picture.
Focus on making deposits.
Prioritize restorative sleep.
Reduce stress where you can.
Flood your body with nutrient-dense foods.
Support your gut.
Stay hydrated.
Lean on your support system.
And don't be afraid to make life easier by choosing nourishing meals that don't require hours in the kitchen.
Healing isn't about perfection.
It's about creating an environment where your body has every opportunity to do what it was designed to do.
One nourishing meal.
One good night's sleep.
One act of self-care at a time.
Frequently Asked Questions
FAQ 1: Do I need to go back to strict AIP elimination during an autoimmune flare?
Not necessarily. If you have successfully reintroduced certain foods and they consistently work well for your body, a flare does not automatically mean you need to remove them again. Instead, it may be more helpful to temporarily avoid foods that feel mildly reactive while focusing on rest, nutrient-dense meals, hydration, and reducing your overall stress load.
FAQ 2: What should I eat during an autoimmune flare?
During an autoimmune flare, focus on warm, nutrient-dense, easy-to-digest meals such as soups, stews, slow-cooked meats, cooked vegetables, bone broth, healthy fats, and gentle starches like sweet potatoes or winter squash. Keeping meals simple can also help conserve energy, which is an important part of supporting recovery.