Where to Start When Your Body Has Stopped Making Sense

Nobody hands you a roadmap when you get an autoimmune diagnosis.

You leave the doctor's office with a name for what's happening inside your body, maybe a prescription, and a whole lot of silence about everything else. What to eat. What to stop eating. Why you feel worse on some days than others. Why "eating healthy" doesn't seem to be doing anything.

I know that silence well. I lived with MS, eczema, and endometriosis for years before I understood that food was either working for me or against me every single day. Not in a vague, wellness-poster kind of way. In a very specific, measurable, felt-in-my-body kind of way.

In April 2020, I made a decision to stop guessing and start paying attention. What followed was one of the most uncomfortable and most transformative periods of my life.

This article is the resource I wish someone had handed me.

A NOTE BEFORE WE START

Everything here reflects general health and wellness education based on published research. It is not individualized medical advice, and it is not a substitute for your relationship with your doctor. Every body is different. Please make any dietary changes in conversation with your healthcare provider, especially if you are managing an active diagnosis or on medication.

THE ELIMINATION PHASE: WHAT THE RESEARCH SAYS (AND WHAT I DID)

The foundation of what I did is called an elimination protocol. The principle is straightforward: remove the foods most commonly associated with inflammation and immune reactivity, give the body time to calm down, then reintroduce foods one at a time to learn what your system actually responds to.

Research on the Autoimmune Protocol (AIP), published in peer-reviewed journals including a 2024 review in Metabolism Open, consistently identifies the same categories of foods as the primary drivers of gut inflammation and immune dysregulation. These are not obscure findings. They show up across immunology, gastroenterology, and nutritional science literature.

Here is what the research flags most consistently, and what I personally chose to remove.

REFINED SUGAR

When blood glucose spikes repeatedly, the body releases inflammatory signals as part of its response. For someone whose immune system is already operating in overdrive, those spikes are not neutral events. Published research links chronic sugar consumption to gut microbiome disruption, increased intestinal permeability, and amplified immune reactivity.

I removed refined sugar completely. That included the "healthier" alternatives like agave and coconut sugar during the strictest phase. Not because sweetness is dangerous, but because my body needed a real reset. I made myself love other flavors like bitter, sour tastes. Your tastebuds are trainable. This is when I switched to having a savory breakfast all the time.

GLUTEN

Research shows that gluten can increase intestinal permeability and trigger inflammatory immune responses even in people without celiac disease. The mechanism that matters most for autoimmune conditions is something called molecular mimicry: gluten's molecular structure is similar enough to certain body tissues that an already-reactive immune system can confuse the two and begin attacking its own cells. This is well-documented in published immunology research and is particularly relevant in conditions like MS, Hashimoto's, and rheumatoid arthritis.

I removed gluten entirely. I still avoid it about 99% of the time, including when I travel in Europe. Yes, even when the bread smells like heaven. I make my own, that does not have gluten, I also make waffles, bagels, you name it and even though it not exactly the same, it is pretty close and I am not missing anything.

DAIRY

The protein in dairy, casein, behaves similarly to gluten when it interacts with a compromised gut lining. When the gut barrier is weakened (which is common in autoimmune conditions), casein can pass into the bloodstream and trigger an immune response. The molecular structure is close enough to certain body tissues that the immune system, already on high alert, can mistake one for the other.

I removed all dairy during my elimination phase. What I noticed when I eventually reintroduced a it was impossible to ignore: the minute I eat dairy, I feel it in my sinuses. Stuffy nose, next morning I am blowing my nose out of nowhere. For years I blamed seasonal allergies. Turns out it was the cheese, yogurt, kifer or cottage cheese the night before.

SEED OILS

Canola, vegetable, sunflower, soybean oils. They are everywhere, and they are marketed as healthy. But they are extremely high in omega-6 fatty acids, which the body metabolizes into pro-inflammatory compounds including prostaglandin E2 and leukotriene B4. Research links chronic high omega-6 consumption to systemic inflammation and disruption of the gut barrier. I replaced all seed oils with olive oil, avocado oil, and coconut oil and have not looked back. I still avoid it as a plague.

NIGHTSHADES

Tomatoes, peppers, eggplant, white potatoes. Genuinely nutritious foods for most people. But they contain compounds called glycoalkaloids that can irritate the intestinal lining, particularly in people who already have gut inflammation. Published research shows a correlation between nightshade consumption and symptom flares in certain autoimmune conditions.

I removed them completely during my strict phase. Tomatoes were one of the first things I brought back. I eat them now, just not every day. Sometimes I eat a bell pepper. But not every week, and not a lot.

CORN

Less commonly discussed, but it was on my personal list. Corn is a frequent hidden ingredient in processed foods, often genetically modified, and can be a reactivity trigger for people with existing gut inflammation. I removed it completely.

PROCESSED FOODS AND ALCOHOL

These two have the most direct documented impact on gut integrity. Research published in Nature identified common emulsifiers found in nearly every packaged food product as disruptors of the intestinal barrier. Alcohol has a similar effect: it compromises the gut lining, allowing bacterial toxins into the bloodstream and triggering systemic inflammation. Both of these went. Fully, for a long time now. I was never a big drinker, just a glass of wine here and there socially. So it was easy for me, it was not a sacrifice but maybe for you it is something you have to see and experiment with. I never thought alcohol was causing any issues for me, but when I removed it entirely I did feel a positive change. My body does not have to neutralize a poison potentially for hours and even days after consuming it. I would much rather have it concentrate on detox, repair and restore.

WHAT I KEPT: EGGS

Eggs stayed on my plate throughout. They are one of the most nutrient-dense whole foods available, rich in protein, choline, and fat-soluble vitamins that support neurological and immune health. The strictest version of the AIP protocol removes eggs in the elimination phase, and some people do better without them. For me, they were a daily staple and I have no regrets. I do from time to time lean into gluten-free vegan recipes and naturally eat less of them but I cannot say that notice a big difference. But that's just me. You have to be your own "doctor" and experiment.

THE REINTRODUCTION PHASE: HOW I FOUND MY WAY BACK

After a few years of strict elimination, I started reintroducing foods carefully, one at a time, watching how my body responded.

This is the part nobody talks about enough. The elimination phase gets all the attention. The reintroduction phase is where you actually learn your body.

NUTS AND SEEDS (SOAKED)

I eat them now, but I soak them first. Raw nuts and seeds contain phytic acid, a compound that binds to minerals and makes them harder for the body to absorb. It can also irritate the gut lining in people with existing digestive sensitivity. Soaking nuts and seeds for 8 to 12 hours in water significantly reduces their phytic acid content, makes them easier to digest, and improves nutrient availability. It is a small extra step that makes a real difference for people whose gut health is still rebuilding. So I either buy the seeds that were soaked before, or I do it myself with most nuts like walnuts. All you have to do is dry them out in low temperature after soaking and they are even more delicious.

DAIRY, OCCASIONALLY

I still largely avoid dairy. But I have brought back small amounts of aged European hard cheeses like Pecorino Romano or Parmigiano Reggiano, maybe once every few months. The extended aging process breaks down most of the lactose, making them significantly easier to tolerate than fresh dairy for many people. I eat them occasionally. I feel the difference when I have too much. That feedback loop is the whole point.

TOMATOES, NOT ALL THE TIME

Back in my life. Not every day, but pretty regularly especially in the summer. I reintroduced them and noticed no reaction. That is what the reintroduction phase is for: finding out what is actually a problem for your body versus what was just part of the reset.

WHAT MAINTENANCE ACTUALLY LOOKS LIKE

The strict phase is not forever. It was never meant to be. The goal was to give my system enough quiet to start healing, and then learn what it could handle long term.

Here is what I want you to hear: once you have done a real elimination phase, your body starts talking to you clearly. You stop guessing. You stop blaming the season, the stress, the age. You start connecting dots you never could before.

My maintenance looks like this: I keep my home clean. I do not stock anything that does not serve me. At a restaurant, I sometimes say yes to something I would not normally eat, and I know exactly what to expect the next morning. That is not failure. That is information.

The belief I keep coming back to: it is not what you eat on an odd day. It is what you eat every day that matters.

BEYOND THE PLATE: REDUCING YOUR TOXIC LOAD

Somewhere along the way I realized I was managing inflammation through food but still absorbing a significant chemical load through everything else touching my body and my home.

So I started there too.

I replaced chemical deodorants with natural ones. Got rid of candles (most conventional candles are made with synthetic fragrance that off-gases continuously into the air in your home). Switched my laundry detergent, cleaning products, and personal care products to cleaner formulations. I stopped getting my nails done at salons.

I still dye my hair. I still wear makeup. But I use apps like Yuka to check ingredient ratings before buying anything. It takes about ten seconds and has completely changed how I shop. I use essential oils instead of synthetic perfumes.

The goal was not perfection. It was to reduce the overall load, so my immune system was not constantly reacting to inputs coming from every direction at once.

You do not have to do all of this at once. Start with food. Food is the biggest lever and where results show up fastest. The environment piece can come later. Just know it exists, and that every layer you address is one less thing your body has to fight.

WHERE TO START

If you want to start but don't know how, this is your starting point.

The research on elimination and reintroduction is consistent, accessible, and published across peer-reviewed journals. What is not always available is someone who has actually done it, lived through the strict years, come out the other side, and can tell you plainly what helped and what did not.

That is what this space is for.

My newsletter goes deeper on each of these pieces, including blood sugar strategy, what to add back and when, and the practical side of building meals that actually work for your body. Come find me there.

And if you are on Instagram, I am at @autoimmune.wellness.method, where I share the research, the real days, and occasionally the finish lines.

Welcome to Glow Wellness Hub. I am glad you are here.

xo

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