For many people, there’s a direct relationship between what you eat and how you feel. (Exhibit A: Feeling an instant mood boost after biting into your favorite dark chocolate bar.) But for people with an autoimmune disease, such as Hashimoto’s, lupus, or arthritis, the connection between food and how they feel can be especially powerful. The root cause of many autoimmune diseases is chronic inflammation, which then manifests in different ways, such as joint pain for one person or recurring migraines for someone else.

The autoimmune protocol (AIP) is an eating plan that was created with this connection in mind. “The AIP is not just a list of foods to avoid [because they cause inflammation]. It centers around foods to eat with all the nutrients the body needs to be healthy,” says Sarah Ballantyne, PhD, a medical biophysicist and a leading expert for the protocol.

The purpose of the eating plan is to reduce the inflammation and pain people with autoimmune conditions may be experiencing. But, like adapting to any new eating plan, it can be overwhelming. Here, Dr. Ballantyne and other experts explain more about what exactly the AIP is and how to do it, if you want to give it a try.

What exactly is the autoimmune protocol?

Nutritional therapy practitioner and Food by Mars founder Alison Marras, NTP, follows the AIP in both her own life and creates recipes helping others do the same. As someone with polycystic ovarian syndrome (PCOS, which is an endocrine disorder but often co-occurs with certain autoimmune diseases) and Hashimoto’s disease, the eating plan has been helpful for her in minimizing flare-ups, which is why she’s so passionate about sharing it with others. Marras explains that the AIP uses three phases to eliminate foods linked to causing inflammation while focusing on foods that are linked to actively fighting inflammation.

Phase one

She explains that phase one is the elimination phase, meant to press the pause button on the most common culprits of inflammation. Grains, legumes, dairy, eggs, refined sugar and sugar substitutes, chemical additives, refined vegetable oils, high-fructose corn syrup, nightshades, nuts, seeds, coffee, and alcohol are all off-limits. There’s no denying that this severely limits what someone can eat, but both Dr. Ballantyne and Marras emphasize that this elimination phase is crucial. Otherwise, it’s almost impossible to pinpoint what foods are causing inflammation in your body.

So what can you eat during the elimination phase? All animal proteins (minus eggs), all vegetables (that aren’t nightshades), moderate amounts of fruit, healthy fats, and grain-free baking flours are still all a-okay.

“The elimination phase can certainly be overwhelming, but it doesn’t have to be done all at once,” Marras says. “You can eliminate eggs one week, cut grains the next, and so forth. Some people find it helpful to just go straight into it while for others gradually is best. It’s important to find what works best for you.”

Phase two

After a month of sticking with phase one, it’s time for phase two. Dr. Ballantyne and Marras explain that phase two is the reintroduction phase, slowly adding back in the foods that were cut out in phase one. This is done in gradual increments since some foods can be more inflammatory for some people than for others. This is why Marras says it’s important to reintroduce foods one at time.

If you reintroduce one food and experience no symptoms after a week of eating it on a regular basis, great! That means that it can continue to be a regular part of your diet on AIP.

Phase three

The last phase of the AIP is the maintenance phase. Now that you’ve identified what foods make you feel great and what foods make you feel not-so-great, you can have fun cooking new meals with everything you feel good about eating. Dr. Ballantyne explains that what you’re left with are nutrient-rich foods that actively help fight inflammation.

“This includes foods rich in protein, fiber, vitamins, minerals, and phytonutrients—which honestly are good food choices for anybody, not just people with autoimmune conditions,” Dr. Ballantyne says.

For all the phases, Dr. Ballantyne emphasizes that lifestyle factors like getting good sleep, managing stress, and being active are also key. “Stress, poor sleep, and being sedentary are all drivers of inflammation,” she says. “I know for me, there are foods I eat on vacation that are totally fine but when I eat them when feeling stressed, it causes a reaction. So it’s important to keep these other factors in mind, too.”

Watch the video below for more information about the link between food and inflammation:

Criticisms and pain points of the autoimmune protocol

While registered dietitian Sharon Palmer, RD, certainly believes in the connection between certain foods and inflammation, she does view the AIP with a skeptical eye. “There’s not enough scientific research to suggest that this is the diet everyone with an autoimmune condition should follow in order to feel better,” she says.

Palmer points out that there is a wealth of scientific evidence showing links between some of the foods the AIP recommends nixing, like sugar and chemical additives, but the jury is still out for some of the others. “Nightshades, for example, [are] very controversial,” she says. “Tomatoes are a type of nightshade but there are also scientific studies showing that people who eat tomatoes experience reduced inflammation.”

Palmer does agree that elimination diets like the AIP can be beneficial in helping someone pinpoint their individual triggers. “If you eliminate gluten, for example, and then notice you feel better, that’s valuable information to have,” she says.

All the experts do agree on one major sticking point, which is that no one should cut out foods that have health benefits unless they absolutely have to. Palmer also strongly recommends working with a registered dietitian who is knowledgeable about the AIP to ensure you’re getting all the nutrients you need while moving through each phase (and beyond). “A dietitian can literally put together an AIP-approved meal plan for someone and help them figure out what meals to make,” she says, rather than you doing that difficult guesswork on your own.

Palmer also recommends working with a dietitian to make sure someone isn’t becoming overly fearful of food. When mealtime can seem like a landmine of potential triggers, it can create a lot of anxiety. She explains that a dietitian can help someone work through these fears so that eating remains the joy- and comfort-filled experience it should be.

“It can be really helpful for people following the AIP to connect with others, whether that’s in Facebook groups or elsewhere,” Marras says. She adds that these communities can become places of support (and a treasure trove of recipe ideas).

Whether you’re launching into phase one or are well into the maintenance phase, Marras says that being diligent about label reading when grocery shopping can be a pain point. “Even if you have your ‘go-to’ products, sometimes a brand will make changes to how something is made and it isn’t always obvious on the front of the packaging,” she says. She found this out the hard way after her daughter, who is highly sensitive to dairy, had a reaction to a snack they’ve long enjoyed as a staple. It took some detective work for Marras to realize the brand changed how the product was made and it now included dairy.

The autoimmune protocol may not be for everyone, but for those with an autoimmune disorder who are looking for an eating plan that can help them manage their pain and inflammation, it is one to consider. Mealtime should never be a stressful or painful experience. The path to reaching that point can look different for different people. What’s most important to remember is that there’s no one perfect way of eating for everyone; the key is to find what works best for you.

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