What to do for a Lyme Disease Flare-Up

Lyme disease healing isn’t usually a linear process. For most patients, recovery from chronic Lyme disease involves ups and downs, including occasional flare-ups that may result from a new treatment (such as introducing a new antibiotic or herb), increased psychological stress, or a lack of sleep, to name a few triggers. 

However, you don’t have to just put up with Lyme disease flare-up symptoms! You can do much from a nutritional and lifestyle perspective to ease your body through the flare-up. 

In this article, I’ll discuss common symptoms that can occur during a Lyme disease flare-up and nutrition and lifestyle strategies that you can use to quench the flare-up and feel better fast! 

Please note that I am an affiliate for some of the products that I’ve linked to in this post. If you click the link here and make a purchase, I may earn a commission, at no extra cost to you.

woman dealing with Lyme disease flare up symptoms of fatigue and joint pain

Lyme Disease Flare-Up Symptoms

I’ve been there myself – brain fog so thick I could barely read two sentences of a book, fatigue that made me feel like the life had been drained out of my body, and achy, stiff joints – a Lyme disease flare-up is no fun at all! 

A Lyme disease flare-up can occur for a couple of reasons. However, two common causes of a Lyme disease flare-up include:

You are experiencing a Herxheimer reaction as a result of treating Lyme disease. A Herxheimer reaction, also referred to as a “die-off” reaction, is defined as “a transient clinical phenomenon that occurs in patients infected by spirochetes who undergo antibiotic treatment.” (1)

In plain English, it is a reaction that occurs when antibiotics (pharmaceutical or herbal) begin killing off Lyme disease in the body, causing the activation of immune system cells and the release of toxic byproducts from the dying bacteria that elicit inflammation.

The Herxheimer reaction is usually transient, but it can be very uncomfortable. That’s why we need to have tools on board for helping our bodies detoxify and reduce inflammation during a Herxheimer reaction. 

Oftentimes, people experience a Lyme disease flare-up when they experience a stressor that compromises the immune system’s ability to Lyme in check.

Examples of stressors that can compromise the immune system and trigger a Lyme disease flare-up include:

  • A lack of sleep
  • Jet lag
  • An acute illness, such as a cold or the flu
  • Working out too hard
  • Mental, emotional, or physical stress
  • Shifts in hormones, such as the hormonal shifts that occur during pregnancy

Early in my healing journey, my Lyme flare-ups always occurred at the end of college semesters. The stress that had built up over each semester always seemed to trigger symptoms for me until I figured out what to do to calm down a Lyme flare-up! Keep reading for my favorite tips for managing a Lyme flare-up. 

Lyme flare-up symptoms can run the gamut. Some of the most common symptoms of a Lyme flare-up include: 

  • Joint pain
  • Increased fatigue 
  • Brain fog
  • Stomach pain
  • Other gastrointestinal symptoms, such as constipation
  • Headaches
  • Sensitivity to bright lights, heat, and noise

This is not a comprehensive list of every possible symptom of a Lyme disease flare-up. However, this article aims to share strategies to alleviate some of the most common Lyme disease flare-up symptoms. 

In my professional opinion, any holistic treatment approach for Lyme disease should include not only medical treatments for Lyme but also supportive treatments that can address Herxheimer reactions and symptoms that tend to rev up during a Lyme disease flare-up. 

What to Do for Common Lyme Flare-Up Symptoms

Are you experiencing a Lyme flare-up? There are steps you can take to mitigate your Lyme flare-up symptoms and start feeling better! Let’s discuss some of the most common Lyme flare-up symptoms and natural strategies you can use to ease the symptoms. 

Lyme and Joint Pain

Achy, cracking necks, knees, and backs are common symptoms of a Lyme flare-up. I remember how my knees used to crack like an elderly person’s joints when I woke up early in my Lyme journey. 

Borrelia burgdorferi, one of the members of the Borrelia bacteria family that causes Lyme disease, loves to hang out in the body’s collagen-rich tissues, including joint tissues. (2)

In fact, hanging out in collagen-rich tissues is one way that Borrelia “hides” itself from your immune system, so it can persist inside your body. When Borrelia hangs out in collagen-containing tissues, the inflammation it triggers can cause aches and pains in those parts of your body. 

While we commonly associate a Lyme flare-up with joint pain, I’ve also found that a Lyme disease flare-up can trigger muscle soreness, stiffness, and pain. 

While pharmaceutical anti-inflammatory and pain-relieving medications, like NSAIDs, certainly warrant a place in our conventional medical system, these drugs come with many side effects. For example, acetaminophen (Tylenol) depletes glutathione (3), a crucial antioxidant that your body needs to fight Lyme disease. (4

Ibuprofen can cause a “leaky gut,” in which gaps develop between cells lining the intestine. (5) A leaky gut allows substances from the gut to leak into the bloodstream, triggering inflammation. (6) That inflammation, in turn, can contribute to chronic pain!

Ironically, ibuprofen use may thereby increase pain over the long term. Alarmingly, anti-inflammatory drugs like ibuprofen are associated with an increased risk of persistent pain! (7)

Fortunately, there are several natural tools that you can try to dampen Lyme-induced muscle and joint pain and achiness: An anti-inflammatory diet, curcumin, and CBD. 

Anti-Inflammatory Diet

Research shows that diet significantly impacts inflammation inside your body, promoting or decreasing it (8). By alleviating inflammation, an anti-inflammatory diet can have a powerful impact on reducing the type of inflammation that drives joint pain during a Lyme disease flare-up. 

I cover the principles of an anti-inflammatory diet for Lyme disease in-depth in my book, The Lyme Disease 30-Day Meal Plan. Pick up a copy of the book for the details!

Several fundamental principles of an anti-inflammatory diet for Lyme disease include avoiding gluten and conventional dairy products from grain-fed animals, reducing refined carbohydrates and added sugars in the diet, and emphasizing anti-inflammatory foods like fatty cold-water fish, cruciferous vegetables, and antioxidant-rich berries, nuts, herbs, and spices. 


Curcumin, a brilliant yellow phytochemical found in turmeric root, has been used for thousands of years in traditional Chinese and Indian medicine for its anti-inflammatory properties. An abundance of research indicates that curcumin can help reduce pain, making it potentially useful for people with Lyme disease who are experiencing joint pain. (9)

Be careful about taking curcumin for joint pain during a Lyme flare-up if you have high oxalate levels because curcumin is naturally high in oxalates. Oxalates are naturally occurring compounds in many foods, primarily fruits, vegetables, nuts, and seeds. 

Generally, our beneficial bacteria will break down oxalates and facilitate their excretion in stool. However, some yeast and other fungi (such as toxic molds) produce oxalate-like molecules.

Therefore, Curcumin may not be the right fit for you if you’ve experienced yeast overgrowth or mold exposure or have had calcium-oxalate kidney stones. 


Cannabidiol (CBD) is a phytocannabinoid, a compound found in plants, including the Cannabis plant, that interacts with our endocannabinoid system (ECS). Our built-in ECS is critical for regulating biological processes throughout our bodies, including mood, immune function, and pain relief. (10

If you try CBD for joint pain, look for either an organic hemp extract containing CBD or a concentrated organic CBD. 

Lyme Disease Fatigue

If your energy is dragging due to a Lyme flare-up, you don’t necessarily need to resort to hanging out in bed until the flare-up passes! You can do several things to increase your energy and ease your body out of the flare-up. 

Take Time to Rest! 

First, give yourself time to rest if you’re experiencing a transient increase in fatigue during a Lyme flare-up. Don’t push yourself with high-intensity exercise, long work hours, or over-scheduling yourself.

Optimize Your Sleep

Sleep has powerful effects on the functioning of your immune system, including your immune system’s ability to fight infections and manage inflammation. Optimizing your sleep, including getting enough sleep and taking steps to ensure the quality of your sleep, is thus essential for easing your body through a Lyme disease flare-up. 

First, make time in your schedule for 7-9 hours of sleep overnight. You may need more sleep than usual during a Lyme flare-up, but try not to oversleep since that may make you feel even more fatigued in the long run. 

Adaptogenic Herbs

Adaptogenic herbs, also referred to simply as “adaptogens,” are herbs that help the body adapt to stress and build resilience. Many adaptogens also happen to increase energy! In my functional nutrition practice, I’ve found that adaptogens can be extraordinarily helpful for individuals dealing with both chronic fatigue and transient fatigue triggered by a Lyme disease flare-up.

There are many adaptogens; some offer gentle energy support, whereas others can be pretty stimulating. When possible, I recommend working with a practitioner to determine the best adaptogen or adaptogen formula to support your needs. 

Examples of adaptogenic herbs that address fatigue include Eleutherococcus, also known as Siberian Ginseng or Eleuthero, Rhodiola, and Schisandra. For more information about adaptogens for Lyme-related fatigue, check out my blog Nutrition, Lifestyle, and Supplements for Lyme Disease and Adrenal Fatigue

Support Your Lymphatic System

Fatigue during a Lyme flare-up can also be caused by the inflammatory response triggered by toxins released from Lyme bacteria, either due to increased disease activity or a killing off of the bacteria by antibiotics. 

Your lymphatic system is a network of vessels and nodes that circulate fluids (including a fluid called “lymph”), cells, and other substances that are part of the immune system throughout your body. When bacteria are killed off, they are ushered to the lymphatic system so that they can be “filtered” from the blood and ultimately disposed of. If a lot of “killing” happens in your body, the lymphatic system can become stagnant, causing fatigue. Modalities supporting lymph flow can sometimes help fatigue during a Lyme flare-up.

Examples of modalities that support the lymphatic system include dry skin brushing (here’s a helpful article on how to dry skin brush), rebounding (jumping on a small trampoline), and taking walks since the pumping action of your skeletal muscles during a walk helps circulate lymphatic fluid. 

Lyme Disease Brain Fog

Are you struggling to think clearly, focus, and concentrate on your work, schoolwork, or other tasks?  If you are, you may be dealing with Lyme “brain fog,” which is exceedingly common in chronic Lyme disease and can also get worse during a Lyme flare-up.

Brain fog isn’t a diagnosable condition, but is a symptom that may stem from brain inflammation caused by Lyme disease.

Several of the natural strategies I’ve discussed so far, including eating an anti-inflammatory diet and optimizing your sleep, can ease brain fog during a Lyme flare-up. However, if you need additional support, you may want to consider adding a binder to your routine.


Taking a binder, or combination of binders, can help alleviate Lyme brain fog. Binders are substances that bind onto toxins in the gut, including toxins released by the bacteria that cause Lyme disease, preventing them from recirculating throughout the body and causing inflammatory symptoms like brain fog. 

Examples of binders include activated charcoal, bentonite clay, and chitosan, to name a few. Binders can be taken in capsules, such as activated charcoal capsules, or in the form of a powder that you mix with water.

Lyme Disease and Stomach Pain

Lyme disease can affect the gastrointestinal system, including the stomach. A flare-up can sometimes cause stomach pain and other symptoms, such as acid reflux and slow stomach emptying. 

Eating a Lyme disease healing diet is the first nutritional step you should take to quell gut symptoms caused by a Lyme flare-up. However, herbal teas that calm the stomach can also be helpful!

Ginger and Peppermint Tea

Herbal teas that soothe the stomach and support stomach motility can help! Ginger can reduce inflammation in the stomach (11) and support gastric motility (12); these effects may relieve stomach pain and associated stomach symptoms, such as uncomfortable sensations of fullness. So if your stomach is feeling off during a Lyme flare-up, try drinking a few cups of ginger tea daily. 

Peppermint tea can also be helpful for an upset stomach. Just be careful with peppermint tea if you have gastroesophageal reflux disease (GERD), as it can relax the lower esophageal sphincter (a flap of tissue between the stomach and esophagus), allowing stomach contents to potentially back up into the lower esophagus and cause irritation. 

Lyme Disease and Constipation

Ah, constipation: That dreaded symptom that nobody wants to experience! Constipation while going through Lyme antibiotic or herbal treatment is a big no-no; you need to have regular bowel movements during your Lyme disease treatment to “take out the trash” generated when pharmaceutical or herbal antibiotics are actively killing Lyme and its co-infections. If you’re struggling with constipation during your Lyme treatment, it’s thus imperative that you get your bowels moving! 

If you’re literally feeling “stuck” in the bowel movement department, here are a few ideas to get things moving: 

Increase Your Fiber Intake

Dietary fiber acts like a broom, sweeping food and waste through your gastrointestinal system, so it can be eliminated promptly from your body. Fiber can also act like a binder, catching toxins in your gut so that they can be eliminated in your poop. 

Many people barely meet the U.S. Dietary Guidelines for fiber intake, about 30 grams daily. However, recent research suggests that even higher intakes of fiber are needed for optimal metabolic health (13) and possibly, for optimal bowel movement activity too! 

In my practice, I recommend aiming for 40-50 grams of fiber per day. It is crucial to increase your fiber intake gradually, especially if you have been eating very little fiber for a long time. 

I recommended prioritizing your dietary fiber from vegetables, fruits, nuts, seeds, and some legumes (if you tolerate legumes) rather than eating boatloads of grains like oatmeal. This is because the dietary fiber in vegetables, fruits, nuts, seeds, and legumes tends to be packaged with other beneficial micronutrients and antioxidants.

Furthermore, these whole-food fiber options are healthier for blood sugar control. In contrast, grains often drive high blood sugar and blood sugar fluctuations while providing little nutritional value.

Examples of foods rich in fiber include dark leafy greens, root vegetables (parsnips, carrots, celery root), and winter squashes like butternut squash, nuts, and seeds. I typically prefer to have people increase their fiber intake through whole foods before resorting to fiber supplements because fiber supplements are not whole foods and don’t offer the additional nutritional benefits we get from whole foods. 


Magnesium can be a godsend for constipation. Some forms of magnesium, such as magnesium citrate, draw water into the colon, helping to induce a bowel movement by keeping stool hydrated. Other forms of magnesium that are better absorbed, such as magnesium glycinate, can also help alleviate constipation but likely do so more by supporting the smooth muscle contractions that move food and waste through the intestines. 

Natural Calm is a form of magnesium citrate that often works well for those with constipation during a Lyme flare-up. 


Staying sedentary in bed or on the couch during a Lyme flare-up can drive constipation because gut motility slows down when our bodies are stationary. Instead, try to weave at least a bit of movement into your day to ease your body out of the flare-up; gentle walking and yoga can make a big difference! 

woman walking to support her lymphatic system
Even a short daily walk can provide powerful support for your lymphatic system, your body’s “garbage disposal” system! If you’re dealing with a Lyme flare-up, supporting your lymphatic system is essential.

Headaches and Lyme Disease

A Lyme disease flare-up can cause headaches for some patients, most likely due to an increased inflammatory response in the nervous system. However, pause before you reach for the nearest bottle of ibuprofen or Tylenol! Research 

Try a Low-Histamine Diet

Histamine is a substance made by cells of your immune system that is involved in allergic responses, inflammation, and the fight against pathogens. Histamine levels in your body can rise when your immune system is dealing with Lyme disease as mast cells, a type of immune cell that releases histamine, increase their activity in the presence of Lyme. (14

High histamine levels can drive headaches and migraines by influencing inflammation in the brain. (15) Reducing histamine levels can thus help some Lyme patients with headaches lessen the frequency and intensity of their headaches. A low-histamine diet is an effective short-term strategy for alleviating headaches. 

What is a low-histamine diet?

A low-histamine diet is a temporary dietary intervention that reduces histamine levels in the body by limiting the intake of foods that naturally contain histamine. It can improve symptoms of high histamine, such as headaches and migraines. The critical thing to note is that the low-histamine diet should be used temporarily; it is not intended to be a long-term diet. 

The low-histamine diet omits the following foods that naturally contain histamine or provoke histamine release from the body and can thus raise histamine levels inside the body:

  • Aged cuts of beef, such as dry-aged steak. Ground beef and stew meat are not usually aged and are unlikely to trigger a histamine reaction. 
  • Fermented foods, including fermented veggies and dairy products 
  • Alcoholic beverages
  • Vinegar
  • Chocolate and cacao 
  • Cured meats
  • Smoked salmon and canned seafood 
  • Bone broth
  • Spinach
  • Tomatoes 
  • Avocado 
  • Bananas
  • Strawberries
  • Citrus fruits

Instead, you’ll focus on eating whole, fresh foods such as fresh meats and poultry, fresh wild-caught seafood, vegetables (other than spinach and tomatoes), fruits (other than avocado, banana, strawberries, and citrus), nutrient-dense starchy carbs like sweet potatoes, root veggies, and squash, and healthy fats like olive oil, pistachios, and macadamia nuts. 

If you’re dealing with mast cell activation syndrome (MCAS) and Lyme disease and are dealing with headaches to boot, the low-histamine diet may benefit you!

Try Magnesium!

Magnesium to the rescue again! Magnesium isn’t only helpful for constipation during a Lyme flare-up; it can also alleviate headaches by reducing inflammation and regulating blood vessel dilation in the brain. Supplemental magnesium glycinate or magnesium malate tends to be most helpful, in my experience, for easing headaches in Lyme disease. 

A dosage of a couple hundred milligrams of magnesium is an excellent start. However, if you notice loose stools, you may need to dial back your magnesium intake. 

Sensitivity to Bright Lights, Scents, Heat, and Noise

Lyme disease can rev up the sympathetic “fight or flight” branch of our nervous system, causing us to feel on edge and sensitive to inputs that generally wouldn’t trigger us, such as bright lights, heat, and noise. During a Lyme flare-up, these sensitivities can increase significantly and make us quite uncomfortable! 

My favorite tool for handling a heightened fight or flight response and sensitivities to bright lights, heat, and noise during a Lyme flare-up is a modality known as “brain retraining.”

Brain Retraining

Brain retraining programs are based on the concept of neuroplasticity and help shift the nervous system out of fight or flight mode into “rest, digest, and repair” mode. When the brain is in “fight or flight” mode, it is more reactive to environmental factors like bright light and noise and substances like food, medications, and supplements. If you feel you’re sensitive to everything, you likely need to engage in a brain retraining program! 

By shifting the nervous system from “fight or flight” into “rest, digest, and repair,” we can ease our sensitivities to environmental inputs during a Lyme flare-up and help our bodies heal. 

Please note that brain retraining is different from mindfulness and meditation practices. It incorporates aspects of these practices but is far more comprehensive. 

Here are a few brain retraining programs that I recommend:

Final Thoughts

Most of us will likely experience a Lyme disease flare-up somewhere along the way in our healing journeys. The more we can be prepared to handle these flare-ups, the more smoothly we can ease our bodies through the flare-up symptoms and feel better faster!

While this article does not provide a comprehensive list of every Lyme flare-up symptom, I hope the tools I’ve shared for common flare-up symptoms will help you if you find yourself in a flare-up. 

If you need more support in your Lyme recovery process, I’d love to work with you one-on-one in my nutrition practice! Having a practitioner at your side who understands Lyme disease and can put together a comprehensive nutrition and lifestyle plan to support your recovery makes all the difference! Schedule a complimentary discovery call with me to learn how I can help!

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