If you've been researching ways to manage an autoimmune condition through food, chances are you've come across both the Paleo diet and the Autoimmune Protocol, or AIP. On the surface, they look almost identical. Both cut out grains, legumes, dairy, and processed foods. Both emphasize whole, nutrient-dense eating. Both trace their roots to the same idea that modern food is doing a number on our health. So what's actually different, and does it really matter which one you choose?
The answer is yes, and understanding why can save you months of frustration and guesswork. Getting this distinction right could be the difference between spinning your wheels and starting to heal.
Paleo: A Better Way to Eat for Most People
The Paleo diet is built around a simple premise: eat the way our ancestors did before agriculture and processed food changed everything. That means quality proteins, vegetables, fruits, and healthy fats, while cutting out grains, refined sugars, legumes, industrial seed oils, and most dairy. For a lot of people, making this shift alone produces significant improvements in energy, digestion, and overall wellbeing.
Paleo works because it removes so much of the modern food supply that stresses the body. When you stop eating processed junk and start eating real, whole food, the inflammatory load drops, blood sugar stabilizes, and the gut gets a chance to breathe.
For the average person looking to clean up their diet, improve their health, or reduce general inflammation, Paleo is a powerful tool. It's also flexible enough to sustain long-term. You can eat eggs for breakfast, throw nuts in your trail mix, enjoy a tomato-based sauce over your protein, and still be following the protocol without issue.
That flexibility is exactly where Paleo and AIP start to part ways. And for people with autoimmune conditions, that gap matters enormously.
AIP: A Therapeutic Protocol, Not Just a Diet
The Autoimmune Protocol was developed specifically for people dealing with autoimmune disease. Where Paleo is a healthier way of eating, AIP is a targeted intervention designed to reduce immune overactivation, heal the gut lining, and identify the specific foods your immune system is reacting to.
People living with conditions like Hashimoto's thyroiditis, rheumatoid arthritis, lupus, inflammatory bowel disease, psoriasis, and dozens of other autoimmune diseases often find that even a clean Paleo diet isn't enough to move the needle on their symptoms. That's because AIP addresses a layer of immune sensitivity that Paleo simply wasn't designed to touch.
AIP takes everything Paleo eliminates and goes further. In addition to grains, legumes, refined sugar, and industrial seed oils, the AIP elimination phase also removes eggs, nuts, seeds, nightshade vegetables (tomatoes, peppers, eggplant, white potatoes), coffee, alcohol, chocolate, food additives, and NSAIDs like ibuprofen. It also restricts seed-based spices, which surprises a lot of people who thought spices were always safe.
This is where people sometimes feel overwhelmed. We understand that reaction completely. But here's the thing: AIP is not meant to be this restrictive forever. It's a two-phase protocol designed to give your body a clean slate and then, through careful reintroduction, help you figure out exactly what you can and can't tolerate long-term.
The Foods That Make All the Difference
One of the most common sources of confusion is around specific foods that are totally fine on Paleo but eliminated during AIP. Let's walk through the big ones.
Eggs are a Paleo staple. They're nutritious, easy to prepare, and convenient. But for people with autoimmune conditions, proteins in egg whites can contribute to gut permeability, so they're one of the first things to go when someone moves from Paleo to AIP.
Nuts and seeds follow similar logic. Most Paleo plans include them as snack foods or cooking ingredients. On AIP, they're removed during the elimination phase because they contain compounds that can irritate the gut lining and drive immune activity in sensitive people.
Nightshade vegetables are another big one. Tomatoes, peppers, eggplant, and white potatoes are all allowed on Paleo but eliminated on AIP. These foods contain alkaloids and lectins linked to increased gut permeability in people with autoimmune dysfunction.
Coffee is eliminated on AIP as well, which stings for a lot of people. It's technically seed-based and contains compounds that can provoke an immune response in certain individuals, which is why it comes out during the elimination phase.
None of this means these foods are inherently bad for everyone. The goal of AIP isn't to scare people away from nutritious food. It's to quiet the immune system so you can assess what your individual body is actually responding to.
AIP Is Structured Around Two Phases
This is a critical distinction that sets AIP apart from nearly every other dietary approach. It's not a permanent list of foods to avoid. It's a two-phase protocol with a clear beginning, middle, and path forward.
The elimination phase typically runs 30 to 90 days depending on the individual and symptom severity. During this phase, you remove all potential immune triggers and flood the body with nutrient-dense foods to support healing. Bone broth, organ meats, leafy greens, fermented foods like coconut kefir and fermented vegetables, and quality proteins become the foundation of your daily eating.
The reintroduction phase follows. This is where AIP gets genuinely interesting, because it transforms the protocol into a personalized experiment in your own biology. You reintroduce eliminated foods one at a time, waiting five to seven days between each addition, and track how your body responds. Some foods come back with no issues. Others reveal themselves as clear triggers, and you end up with a customized eating plan built around what your body can and can't handle.
That personalized roadmap is something Paleo, despite all its benefits, simply doesn't offer. AIP gives you the data your body needs to build a sustainable eating plan for the long haul.
Why Getting This Right Actually Matters
Choosing between Paleo and AIP isn't just a matter of personal preference. For someone without an autoimmune condition, Paleo is likely more than sufficient and genuinely life-changing. It removes so much of what's working against the average body that most people feel dramatically better within weeks.
For someone with an autoimmune diagnosis or persistent symptoms that haven't responded to other interventions, following a standard Paleo diet while missing the AIP piece can lead to months of minimal progress. We've heard from many people in our community who cleaned up their diet, went Paleo, and were frustrated when they still felt unwell. Moving to AIP was the missing piece.
The stricter elimination isn't about perfection or deprivation. It's about giving an already taxed immune system the break it needs so the real healing work can begin.
Where Eat G.A.N.G.S.T.E.R. Fits In
One of the hardest parts of starting AIP, especially if you're coming from a Paleo mindset, is baking. Paleo baking leans heavily on almond flour, eggs, and seed-based ingredients. That covers a significant portion of the baking playbook, and it all goes away during AIP elimination. Even something as simple as weekend pancakes requires a completely different approach.
Our baking mixes are built specifically for this. We use tiger nut flour, a root vegetable that's completely AIP compliant, as our base. There are no eggs required, no nuts, no seeds, no nightshades, and no artificial additives. Our products are also certified gluten-free and made in a facility free from the top 14 allergens, so you can make pancakes, cakes, muffins, cookies, and breads that fit the AIP elimination phase without compromise.
Whether you're in week one of your elimination phase or you've been navigating AIP for years, having go-to baking options that you can trust makes the whole process feel a lot more sustainable. Browse our full collection of baking mixes and find what works for your kitchen. Food should still bring joy, even when you're healing.
The Bottom Line
Paleo and AIP share a foundation, but they serve different purposes. Paleo is a long-term lifestyle approach that removes most of the modern food supply's worst offenders. AIP is a structured, therapeutic protocol specifically designed for people with autoimmune conditions who need to go further. Understanding which one you actually need can make the difference between slowly feeling better and finally getting real answers.
If you've been following Paleo and still struggling, AIP might be your next step. We're here to help make it as uncomplicated as possible. That's what we've always been about.
