If you've been diagnosed with an autoimmune condition or you're dealing with chronic inflammation, you've probably stumbled across a confusing alphabet soup of dietary protocols. AIP, Paleo, Whole30—they all sound similar, they all seem to eliminate a lot of foods, and honestly, it's hard to figure out which one is right for your situation. We get it. When you're already overwhelmed by symptoms and doctor's appointments, the last thing you need is more confusion about what you should be eating.

Here's the thing though: while these diets share some common ground, they're actually designed for very different purposes. Understanding the distinctions between them isn't just academic—it can mean the difference between a diet that helps you heal and one that leaves you frustrated and still struggling with symptoms. We've worked with countless people in our community who've tried one approach when they really needed another, and we want to save you that trial and error. Let's break down what makes each of these protocols unique, who they're designed for, and how to figure out which one might be your best path forward.

The Paleo Diet: Where It All Started

The Paleo diet is probably the one you've heard about the most. It's been around longer than the others and it's based on a simple premise: eat like our prehistoric ancestors did. That means focusing on whole, unprocessed foods that would have been available to hunter-gatherers before agriculture changed everything about 10,000 years ago.

On Paleo, you're eating meat, fish, vegetables, fruits, nuts, and seeds. You're avoiding grains, legumes, dairy, refined sugar, and processed foods. The thinking behind Paleo is that our bodies haven't evolved to properly digest many of the foods that came with agriculture, and that going back to a more ancestral way of eating can improve overall health, energy, and body composition.

Paleo isn't specifically designed for autoimmune conditions. It's more of a general wellness approach that a lot of people use for weight loss, athletic performance, or just feeling better overall. You'll still eat eggs on Paleo. You can have nuts and seeds. Nightshade vegetables like tomatoes and peppers are totally fine. For someone without autoimmune issues or significant food sensitivities, Paleo can be a great way to clean up your diet and ditch processed junk.

But here's where it gets tricky for those of us with autoimmune conditions: while Paleo eliminates some problematic foods, it still includes several that can trigger immune responses and inflammation in sensitive individuals. Eggs are one of the most common food sensitivities for people with autoimmune disease. Nuts and seeds contain compounds that can irritate the gut lining. Nightshades contain alkaloids that some people react to badly. So while Paleo is a solid foundation, it's often not restrictive enough for true autoimmune healing.

Whole30: The 30-Day Reset

Whole30 takes Paleo and adds some extra rules, but with a completely different philosophy. This isn't meant to be a forever diet—it's a short-term elimination protocol designed to reset your relationship with food and help you identify how different foods affect your body.

On Whole30, you're eliminating the same foods as Paleo, but you're also cutting out all added sugar (even natural sweeteners like honey or maple syrup), alcohol, and anything that tries to recreate baked goods or treats, even if they use compliant ingredients. So no Paleo pancakes, no banana ice cream, no almond flour cookies. The idea is to break the psychological grip that sweet treats and comfort foods have on you, and to stop using food as a reward or emotional crutch.

The Whole30 program lasts exactly 30 days, and during that time, you're not supposed to weigh yourself or take body measurements. It's not about weight loss, even though a lot of people do lose weight. It's about figuring out which foods make you feel good and which ones don't. After the 30 days, you systematically reintroduce eliminated food groups one at a time to see how your body responds.

Whole30 can be really helpful if you suspect you have food sensitivities but you're not sure which foods are the problem. It's also great if you've developed unhealthy eating patterns and need a hard reset. But like Paleo, Whole30 wasn't specifically designed for autoimmune disease. It still includes eggs, nuts, seeds, and nightshades. And because it's only 30 days, that's often not enough time for someone with a serious autoimmune condition to see significant healing. Gut repair and immune system regulation can take months, not weeks.

AIP: The Autoimmune Protocol

This is where things get more targeted. The Autoimmune Protocol, or AIP, was specifically designed for people with autoimmune diseases. It's not a general wellness diet or a short-term reset—it's a therapeutic protocol aimed at reducing inflammation, healing the gut, and calming an overactive immune system.

AIP starts with a much stricter elimination phase than either Paleo or Whole30. You're cutting out grains, legumes, dairy, refined sugar, and processed foods, just like the other two. But you're also eliminating eggs, nuts, seeds, nightshades, and certain spices and food additives that can be problematic for autoimmune conditions. We're talking about foods that might be perfectly healthy for most people but that contain compounds known to increase intestinal permeability or provoke immune responses in susceptible individuals.

The elimination phase of AIP typically lasts at least 30 days, but often much longer—usually 60 to 90 days or until symptoms significantly improve. The goal isn't just to avoid trigger foods forever. Once you've given your body time to heal, you start a careful reintroduction process, adding back eliminated foods one at a time to see which ones you can tolerate and which ones need to stay out of your diet long-term.

What makes AIP different isn't just what you eliminate, though. It's also about what you emphasize. AIP puts a huge focus on nutrient density—eating organ meats, bone broth, fermented foods, and a wide variety of vegetables to flood your body with the vitamins and minerals it needs to repair and regenerate. It's not just about avoiding bad stuff but actively healing with good stuff.

AIP also recognizes that food is only part of the equation. The protocol includes lifestyle factors like stress management, sleep quality, and gentle movement, because we know that you can eat perfectly and still struggle if you're chronically stressed or sleep-deprived.

The Key Differences at a Glance

So let's make this really clear. Paleo allows eggs, nuts, seeds, and nightshades. Whole30 allows eggs, nuts, seeds, and nightshades but removes added sweeteners and treats. AIP eliminates eggs, nuts, seeds, nightshades, and takes the most comprehensive approach to removing potential immune triggers.

Paleo is indefinite and lifestyle-based. Whole30 is exactly 30 days followed by reintroduction. AIP has an elimination phase that lasts as long as needed for healing, followed by a systematic reintroduction process that's customized to your individual responses.

The purpose is different too. Paleo is about general health and ancestral eating principles. Whole30 is about breaking bad habits and identifying food sensitivities. AIP is specifically therapeutic, designed to address autoimmune disease at the root level by healing the gut and regulating immune function.

Which One Is Right for You?

Here's how we think about it. If you're generally healthy, you just want to eat cleaner and feel better, and you're not dealing with autoimmune issues or serious inflammation, Paleo is probably your best bet. It's sustainable long-term, it's less restrictive than the others, and it gives you a solid nutritional foundation without being overly complicated.

If you suspect you have food sensitivities or you've developed unhealthy relationships with certain foods, and you want a structured reset that will help you identify problem areas, Whole30 might be your answer. It's short-term, it's got clear rules, and there's a big community and tons of resources to support you through the 30 days.

But if you've been diagnosed with an autoimmune condition—whether that's Hashimoto's thyroiditis, rheumatoid arthritis, lupus, Crohn's disease, ulcerative colitis, psoriasis, or any of the other 80-plus autoimmune diseases out there—AIP is really the protocol designed with you in mind. It's more restrictive, yes, but that restriction is purposeful and temporary. It's giving your body the best possible chance to heal by removing all the foods most likely to be triggering inflammation and immune responses.

We've seen people try Paleo or Whole30 when they really needed AIP, and they end up discouraged because they're still having symptoms. They think eliminating grains and dairy should be enough, but they're still eating eggs every morning and almond butter every afternoon, and those foods are secretly keeping their immune system fired up. Then they try AIP and finally, finally, things start to shift. The brain fog clears. The joint pain eases. The digestive issues calm down. That's when they realize the extra restriction was worth it.

What About Baking and Treats?

This is where people get really confused, and honestly, it's one of the most frustrating parts of following any of these protocols. When you're on Paleo, you can make cookies and brownies with almond flour and eggs. You've got tons of options. When you're doing Whole30, you're specifically told not to make treat versions of things, even if the ingredients are technically compliant. And when you're on AIP, you can't use eggs, nuts, or most of the flours that conventional baking relies on.

That's exactly why we created our line of AIP-compliant baking mixes. We understand that eliminating foods for healing doesn't mean you should feel deprived or excluded from the simple joy of a warm cookie or a slice of birthday cake. Our mixes use ingredients like cassava flour and tigernut flour that are AIP-compliant, and they're specifically formulated to give you that texture and flavor you're missing without any of the immune triggers.

Whether you're making our Double Chocolate Brownie Mix, whipping up a batch of Snickerdoodle Cookies, or baking Chocolate Chip Cookies, you're getting treats that fit within the AIP framework. You're not cheating or undermining your healing. You're just making life on a restrictive diet a little bit sweeter, which is something you absolutely deserve.

Starting Your Journey

If you're standing at the beginning of this journey trying to figure out which protocol to follow, we'd encourage you to be honest about where you are and what you need. Don't minimize your symptoms or convince yourself that you can get by with something less restrictive if you truly have an autoimmune condition. AIP might look intimidating from the outside, but the results speak for themselves.

At the same time, don't feel like you have to be perfect. We've both been through this ourselves, and we know how hard it is. Start where you are. Make the changes you can make today. Use resources and products that make the transition easier. And remember that this elimination phase isn't forever—it's a temporary healing period that gives you the information and the foundation you need to build a sustainable, personalized diet that works for your unique body.

Whether you choose Paleo, Whole30, or AIP, you're taking a powerful step toward better health. You're choosing real food over processed junk. You're listening to your body instead of ignoring its signals. And you're investing in your long-term wellbeing in a way that really matters. We're here to support you every step of the way, with products that make the journey easier and a community that understands exactly what you're going through.