Autoimmune Disease & Long COVID: Understanding Symptoms, Treatments, and How to Feel Better

by Sarah Day Spangler, RPh, Founder of The EveryDay Pharmacist and Krista Day-Gloe, LCSW, Founder of Healing Roots Wellness Center

If you’ve been living with unexplained fatigue, stubborn inflammation, or a long list of symptoms that just won’t go away, you’re not alone — and you’re definitely not imagining it. Many people today are navigating conditions where the immune system is working against them instead of protecting them. Whether you’ve been diagnosed with an autoimmune disease or are dealing with lingering symptoms months after COVID-19, it can feel frustrating, confusing, and exhausting.

Here’s the good news: understanding what’s going on inside your body is the first step toward feeling better. In this post, we’ll break down what’s really happening, what symptoms to watch for, how autoimmune disease and Long COVID can overlap, and — most importantly — what you can do to start supporting your body on the path to healing.

When Your Immune System Gets Confused

Your immune system’s main job is to keep you safe — to recognize viruses, bacteria, and other invaders and get rid of them before they make you sick. But sometimes, that defense system goes off track. In autoimmune disease, your immune system becomes confused and starts attacking your own cells as if they were the enemy.

There are more than 80 known autoimmune conditions — including rheumatoid arthritis, lupus, Hashimoto’s thyroiditis, multiple sclerosis, psoriasis, and inflammatory bowel disease. Each one looks a little different, but they all have one thing in common: chronic inflammation that’s directed at your own body.

Krista often explains this process to clients using the Cell Danger Response, a concept developed by mitochondrial researcher Dr. Robert Naviaux. “When a cell senses danger — whether from infection, toxin exposure, trauma, or even chronic stress — it throws up its shields,” Krista says. “This is a brilliant short-term survival response. The problem is, when those cells stay on high alert too long, they start blocking communication with other cells — even with the medications and nutrients meant to help them heal.”

In other words, the body gets stuck in protection mode. Healing often requires a combination of medical support, lifestyle changes, and nervous system regulation to teach those cells that they’re safe again.

Symptoms That Shouldn’t Be Ignored

Autoimmune diseases can affect just about any organ or system, which is why symptoms can look so different from person to person. Most people notice a mix of things like:

• Fatigue or low energy — even when you’re getting enough sleep
• Joint pain, swelling, or stiffness — especially in the morning
• Muscle aches or weakness
• Skin changes — rashes, dryness, or unexplained discoloration
• Digestive issues — bloating, diarrhea, constipation, or nausea
• Low-grade fevers or getting sick more often
• Brain fog — forgetfulness, poor focus, or mental fatigue
• Numbness or tingling — often in hands, feet, or face

It’s also common to have “flares” — times when symptoms suddenly get worse — followed by calmer periods. Stress, illness, certain foods, or even lack of sleep can trigger these flare-ups.

Krista notes, “It’s easy to blame ourselves when our symptoms return — like we must’ve done something wrong — but these flares are the body’s way of saying, ‘I still don’t feel safe.’ They’re signals, not failures.”

The Long COVID Link

After a COVID-19 infection, many people experience symptoms that linger for weeks or even months. This is called Long COVID (or post-COVID syndrome), and interestingly, it can look very similar to autoimmune disease. Researchers believe that in some people, COVID can even trigger an autoimmune-like reaction — either by waking up a condition that was already brewing or by starting something new entirely.

Common Long COVID symptoms include:

• Deep, relentless fatigue that worsens with activity
• Brain fog — slowed thinking, memory problems, or trouble concentrating
• Shortness of breath or chest tightness
• Muscle or joint pain
• Heart palpitations, rapid heartbeat, or dizziness
• Sleep issues and mood changes
• Digestive problems, altered taste, or smell changes

If symptoms like these stick around for more than three months after COVID — especially if they’re interfering with daily life — it’s worth talking to a healthcare professional. Sometimes, what looks like “just lingering effects” is actually your immune system still stuck in overdrive.

Steps Toward Relief That Really Help

There are many suggestions to help alleviate the symptoms — from diet changes to stress reduction. We’ll explore some of the advice that’s out there and break down why it can be helpful. But let’s remember: we are not doctors, and this is not medical advice. Our goal is to provide you with education and tools to explore your health and mind-body connection alongside your healthcare professionals.

Medication is often part of the picture, but lifestyle changes can make a big difference in how you feel day to day. Healing from autoimmune disease or Long COVID isn’t about one fix — it’s about finding the right combination of supports that help your body return to safety and balance.

Anti-Inflammatory Foods — But Mindfully

Let’s start with one of the biggest recommendations: looking at your relationship with food. A lot of lifestyle advice begins with diet — and for good reason. What we eat can influence inflammation, energy, and gut health. But as Krista emphasizes, “food isn’t the enemy — it’s the body’s relationship to food that often needs healing.”

Removing foods can be incredibly helpful once specific triggers are identified for your unique body, but doing so without medical guidance can become a slippery slope. “We always encourage people to work with a dietitian or medical professionals alongside us,” Sarah says. “Without the right medications or supplements on board, removing foods can backfire — your body may still stay in defense mode.”

Krista adds, “Unfortunately, many autoimmune symptoms show up in the digestive tract, making it feel like it’s all about the food. But often, it’s more about how the body is reacting to food in a stressed or inflamed state. When medications or healing supports calm that inflammation, we can finally see whether it was truly about the food — or not.”

We know food recommendations can be confusing! Even whole foods can feel contradictory — eggs, for example, seem to take turns being the hero or the villain every year. That’s why we stay away from labeling foods as ‘good’ or ‘bad.’ All foods can have a time and place within a balanced plan, depending on what your body needs in the moment.

This is why we urge our clients not to do this work on their own, but rather with someone trained in autoimmune conditions and the relationship between food and inflammation. There’s a lot of advice that can work for some but definitely not for others — so please find someone to help you tease apart all the information out there!

The Gut Health Connection

Your gut isn’t just about digestion — it’s home to roughly 70% of your immune system. A healthy gut microbiome helps regulate immune responses, reduce systemic inflammation, and maintain a balanced “on/off switch” for immune activity. When the gut is out of balance (often called dysbiosis), it can fuel autoimmune flares, worsen post-viral symptoms, and even contribute to “leaky gut,” where inflammatory molecules pass into the bloodstream and keep the immune system on high alert.

“From a nervous-system perspective,” Krista adds, “the gut also mirrors our emotional landscape. When the body is in chronic fight-or-flight, digestion shuts down — the body literally can’t rest and repair.”

Prioritizing gut health and working with a dietitian can help address what may be causing inflammation in your body, strengthen this barrier, and help your immune system find its balance again. Sometimes, the right medication or supplement support helps the gut calm enough to let these foods do their job.

Make Sleep a Priority

Both autoimmune activity and post-viral recovery require more rest than usual. Quality sleep supports immune balance, hormone regulation, and tissue repair. When you push through fatigue, it signals the body that danger is still present. “Think of rest as the most productive thing you can do for your cells,” says Krista. “It tells your body: it’s safe to heal.”

Calm Your Stress Response

Many times, people focus on the bigger coping skills like journaling, going to a workout class, or taking long walks — but for some, even those can feel too big. That’s why we start small. Checking in with your breath a few times a day and exhaling a bit longer than you inhale can be just as effective as a 60-minute workout.

Chronic stress throws your immune system even more off balance. Gentle practices like meditation, yoga, massage, breathwork, or short walks can help shift your body out of “fight or flight” mode. You don’t need a perfect mindfulness practice — even a few deep breaths can help your cells register that the danger has passed.

Move, But Don’t Overdo It

Low-impact movement — stretching, walking, tai chi, or water exercise — keeps your joints and circulation healthy. But pushing too hard can backfire, especially if you’re dealing with post-exertional crashes from Long COVID.

Krista often helps clients track their energy and activity patterns to avoid “boom-and-bust” cycles. On days that patients feel well, they often want to “get everything done” that they couldn’t during a flare. But that burst of energy can backfire and send the body right back into a flare. The goal is to work with your body, not against it.

Track Your Patterns

Keep a simple symptom journal. Note what you eat (if that feels helpful and you have someone you trust supporting you in this area), how you sleep, your activity level, and how you feel. Patterns often emerge that can guide your care and help identify triggers. Journaling can also help you communicate with your care team, especially when symptoms fluctuate.

Medications That May Be Part of Your Plan

Because autoimmune conditions are driven by an overactive immune response, medications often focus on calming that inflammation, slowing disease progression, and protecting organs. Some of the most common options include:

• NSAIDs (like over-the-counter ibuprofen or naproxen): Reduce inflammation and pain.
• Corticosteroids (like prednisone): Quickly control inflammation during flares.
• DMARDs (like methotrexate or azathioprine): Help slow or stop disease progression.
• Biologic therapies (like Humira, Remicade, or Rituximab): Target specific parts of the immune system.
• JAK inhibitors: Block inflammatory signals inside immune cells.

The right treatment plan depends on your condition, severity, and overall health — and it’s often a combination of medications plus lifestyle support. The goal is to quiet the immune system enough to let your body heal without suppressing it more than necessary.

“Medications can help reduce the body’s inflammation and restore communication between cells,” Sarah says. “But we also need to make sure those cells are ready to receive that help — which is where stress management, nutrition, and mental health care play a role.”

And remember, any pharmacist recommendations about your medications should be discussed with your physician or other healthcare providers. Open communication ensures the safest and most effective medication therapy for your individual needs.

Healing Is a Process — and You’re Not Alone

Living with an autoimmune condition or Long COVID can feel like an uphill climb. But healing is possible — and it’s often a gradual process made up of small, meaningful steps. Many people improve significantly with the right combination of treatment, daily habits, and ongoing support.

The most important thing you can do is listen to your body. If something feels off, don’t ignore it. Keep communicating with your care team, advocate for yourself, and give yourself permission to move at your own pace.

Partner With The EveryDay Pharmacist

Managing medications for autoimmune disease or Long COVID can be complicated — but you don’t have to figure it out on your own.

As a clinical pharmacist, Sarah works one-on-one with patients to simplify treatment plans, explain what each medication is doing, and help you make confident, informed choices about your health.

At Healing Roots Wellness Center, Krista and her team help clients understand the body’s signals, reduce nervous-system overwhelm, and support the mind-body connection that makes medication and lifestyle changes more effective.

Ready to take the next step?
Schedule a personalized medication review with The EveryDay Pharmacist and get the support you need to feel better — and stay better.