You’ve cleaned up your diet, cut out gluten, started buying organic when you can, and made an effort to choose the “healthy” options at the grocery store. Maybe you’re drinking more water, taking supplements, and paying closer attention to what goes on your plate than ever before. So when you’re still dealing with fatigue, brain fog, digestive issues, joint pain, skin symptoms, or autoimmune flares, it’s understandable to wonder: What am I missing? I’m here to suggest that it might be ultra-processed foods.
That’s one of the most frustrating parts of living with an autoimmune condition. You can put a lot of time and effort into trying to support your health and still feel like your body isn’t responding the way you hoped. At that point, it’s easy to start searching for the one thing you need to cut out. Maybe the answer is the one ingredient, food group, or dietary rule that will finally explain why you still don’t feel well.
Sometimes, it’s worth stepping back before adding another restriction. Instead of focusing only on whether a particular food is gluten-free, dairy-free, low-carb, high-protein, or packed with added nutrients, we can look at the bigger picture of what we’re eating overall. This is where ultra-processed foods become an important part of the conversation.
A food can check all the boxes we’ve been taught to look for and still be highly processed. A protein bar may be gluten-free and high in protein. A frozen meal may be organic and low in calories. A snack may be plant-based and fortified with vitamins. Those labels can tell us something useful, but they don’t necessarily tell us the whole story about how that food might react with your specific body and autoimmune condition.
The goal isn’t to obsess over finding the “perfect” food or blame every symptom on what you ate for breakfast. It’s to look at patterns and ask broader questions about how your nutrition may be interacting with other parts of your health, including your gut, immune system, nutrient status, lifestyle, and individual symptoms. Could the amount of ultra-processed food in your diet be one piece of the puzzle? For some people, it may be worth taking a closer look.
What exactly are ultra-processed foods?
“Processed” and “ultra-processed” aren’t necessarily the same thing. Almost all food undergoes some type of processing. Washing, freezing, cooking, fermenting, drying, or grinding food are all forms of processing, and none of those things automatically make a food unhealthy (and yes, please wash your vegetables before eating them, even if it means they are now “processed”).
Ultra-processed foods are different. They’re typically industrially formulated products made with ingredients and additives that you wouldn’t ordinarily use in a home kitchen. Think things like packaged snack foods, sugary cereals, many fast-food products, certain frozen meals, processed meats, sweetened beverages, and some highly formulated “health” foods.
And this is where things can get a little tricky, because a product can have a health-focused label on the front and still be highly processed. “Gluten-free,” “low-fat,” “high-protein,” “keto,” “plant-based,” and “natural” may tell you something about a product, but they don’t necessarily tell you how nutrient-dense or minimally processed it is.
That’s why it can be helpful to look at the whole food, rather than relying solely on the marketing on the package.
So, can ultra-processed foods cause autoimmune disease?
This is where we need to be careful. There isn’t enough evidence to say that eating ultra-processed foods directly causes autoimmune disease.
Autoimmune conditions are complex. Genetics, infections, environmental exposures, gut health, immune regulation, hormones, nutrition, stress, sleep, and other factors can all play a role. Research has found associations between higher consumption of ultra-processed foods and a variety of chronic health conditions, and researchers are increasingly interested in how dietary patterns and highly processed foods may influence inflammation, metabolic health, and the gut microbiome.
For someone already dealing with autoimmune disease, that makes the quality of the overall diet increasingly important. Rather than asking, “Is this food causing my autoimmune disease?” a more useful question might be, “Could my current diet be contributing to some of the factors that are making it harder for my body to regulate inflammation?”
That’s a very different question, and it’s one we can actually investigate.
Your gut and your immune system are connected
If you’ve spent any time learning about functional medicine, you’ve probably heard that gut health matters. There’s a reason for that. Your gastrointestinal tract is not simply a tube that moves food through your body. It interacts closely with your immune system and houses trillions of microorganisms that make up your gut microbiome.
Your diet helps shape that environment. A diet centered around a variety of minimally processed, fiber-rich plant foods provides a wide range of nutrients and compounds that can support a healthy gut ecosystem. On the other hand, a diet dominated by highly processed foods may provide fewer of the fibers and micronutrients that support a diverse and healthy microbiome.
Some ultra-processed foods also contain additives or formulations that researchers are investigating for their potential effects on the intestinal environment. That doesn’t mean every additive is damaging or that one packaged food is going to “destroy your gut.” It means the overall dietary pattern matters.
If most of your meals and snacks come from highly processed foods, there may be an opportunity to improve the nutritional foundation of your diet.
But what if you’re eating “healthy” processed foods?
This is one of the biggest things I see people get hung up on. You don’t have to eat cookies, chips, and fast food every day to have a diet that is relatively high in ultra-processed foods.
Maybe your breakfast is a protein shake made from a highly formulated powder. Your lunch is a gluten-free frozen meal, your afternoon snack is a protein bar, and dinner is a packaged “healthy” meal replacement. None of these foods are automatically bad, and they may be incredibly useful at times.
If you’re traveling, working long hours, caring for kids, or simply having a day where cooking isn’t happening, a protein bar is a lot better than skipping a meal entirely. The goal isn’t perfection. But if highly formulated foods make up the majority of your diet, you may be missing an opportunity to give your body more of the nutrients and food components it needs. That need for certain nutrients might be showing up specifically in those symptoms you fight on the daily.
A quick caveat: there are better protein bars out there than others. Some come with less processing and less overall additives and such. If possible, choosing those options for those crazy days will help in the long run as well. The idea is choosing maybe a better option if the “best” option (whole foods) is not possible.
Your “healthy” diet may also need to be individualized
This is another reason I don’t believe in a one-size-fits-all autoimmune diet. Two people can eat the exact same food and have completely different experiences.
One person may tolerate dairy beautifully while another notices digestive symptoms after eating it. One person may feel great eating legumes while another has difficulty digesting them. And sometimes the issue isn’t even the food itself. It may be the person’s current gut health, nutrient status, stress load, sleep, digestive capacity, or other underlying factors that influence how they respond to certain foods.
This is why functional medicine looks at the whole picture. Instead of handing you a generic list of “inflammatory foods” and sending you on your way, we can look at your symptoms, health history, lifestyle, nutrition, labs, and other potential contributors.
The goal isn’t to create a diet that looks perfect on paper. It’s to find an approach that makes sense for your body and your circumstances.
So, do you need to give up ultra-processed foods completely?
Probably not. And I don’t want you walking away from this blog thinking you need to throw everything in your pantry into the trash.
Food should also be practical and enjoyable. There will be busy days, birthdays, vacations, and nights when dinner comes from a box. That’s life. Instead of aiming for “never,” consider asking yourself, “What percentage of my diet is made up of whole and minimally processed foods?”
Then look for small opportunities to shift that balance. Could your packaged breakfast become eggs and fruit a few mornings a week? Could you add berries and nuts to your snack instead of relying on a bar every afternoon? Could you swap a packaged side for roasted vegetables? Could you cook one extra batch of protein on the weekend so weekday meals are easier?
Small changes can add up.
Start with progress, not perfection
If you have an autoimmune condition, you already have enough to think about. You don’t need another list of 47 foods you’re “not allowed” to eat. Instead, start small. Look at one meal, then another. Try adding something colorful to your plate, choosing a whole-food protein, adding a source of fiber, or swapping one highly processed snack for a minimally processed option.
Pay attention to how you feel, not because every symptom is automatically caused by food, but because your body is giving you information worth noticing.
Your diet is one piece of the larger picture of your health. If you’re doing everything you can to feel better, but still feel like you’re missing something, you don’t necessarily need another restrictive diet. You may need someone to help you step back, look at the bigger picture, and investigate what could be contributing to how you’re feeling.
I would love to be the next step in getting you closer to thriving, and not just surviving. Reach out today!
Sources:
Elizabeth, L., Machado, P., Zinöcker, M., Baker, P., & Lawrence, M. (2020). Ultra-Processed Foods and Health Outcomes: A Narrative Review. Nutrients, 12(7), 1955. https://doi.org/10.3390/nu120719
Monteiro, C. A., Cannon, G., Levy, R. B., Moubarac, J. C., Louzada, M. L., Rauber, F., Khandpur, N., Cediel, G., Neri, D., Martinez-Steele, E., Baraldi, L. G., & Jaime, P. C. (2019). Ultra-processed foods: what they are and how to identify them. Public health nutrition, 22(5), 936–941. https://doi.org/10.1017/S1368980018003762
