by Jenny Lelwica Buttaccio
Posted 5/1/20

Anyone beginning a new herbal protocol for Lyme disease is bound to have questions. After all, if you’ve been taking a variety of prescription medications for a while, switching to a natural regimen can feel like a leap of faith. Will the new protocol be one that you can tolerate? How will you handle die-off reactions or detoxing? How long will it take to work?

To help you answer these questions and more, we turned to Dr. Bill Rawls, MD, Medical Director of RawlsMD and Vital Plan, who has experienced chronic Lyme firsthand. We also scoured the research and other reliable sources to create a resourceful guide to getting started, plus offer suggestions for tackling some of the more common pitfalls patients encounter.

One overarching bit of advice to remember: When implementing a new protocol, starting low and going slow is often a critical step to sustaining any health regimen over the long haul. If you hit a roadblock along the way, try not to panic. You can always press the pause button and give your body a chance to reset.

1: Do I Need To Quit My Other Treatments Before I Start a Natural One?

First, it’s important to note that there’s a time and a place for the use of medications in the treatment of Lyme disease and Lyme coinfections. But there’s one problem with antibiotic use, especially some of the broad-spectrum ones used to treat tick-borne diseases: They’re not very discriminative about the types of bacteria they kill. In addition to the pathogens, they zap the healthy flora in your microbiome, too.

“When you look at the microbes that are associated with Lyme disease, you’ve got a short window of opportunity that’s directly after the infection,” explains Dr. Rawls. “When they enter the body, they begin to disseminate through it. That’s the critical time frame to hit them with antibiotics, and it might knock down their counts enough that the immune system can take over.”

Image split in half. One side, Close-up of abundance pills. Other side, bowls of herbal medicine ingredients.

But approximately 10%-20% of people who receive treatment for early Lyme disease continue to have symptoms, indicates an article in the The New England Journal of Medicine. And, that’s not factoring in the people whose disease advanced to later stages due to misdiagnosis or delayed diagnosis.

While some healthcare providers may be inclined to continue with the use of synthetic antibiotics (and in some cases, that may be warranted), problems tend to arise with your gut’s micro-ecosystem the more aggressive an antibiotic protocol is. As your microbiome becomes imbalanced, you might experience:

“Ideally, I’d like to see people get well using only herbal therapies, because they are restorative to the body, support healing, and don’t disrupt your microbiome,” says Dr. Rawls. However, if your current treatment includes antibiotic therapies, or if you’re shifting from antibiotics to an herbal antimicrobial protocol, the herbs can help smooth your experience.

That’s because herbs help to normalize the body’s processes, such as restoring gut flora, improving sleep and energy levels, balancing hormones, and supporting immune function. And because they have a low risk of toxicity, herbs can often be used in combination with medications, explains Dr. Rawls. Plus, using herbs may allow you to use less medication or minimize undesirable side effects that drugs can cause.

However, remember that you and your doctor are a team, so you should consult with them before you replace medications with natural therapies or add them to an existing regimen.

2: When Should I Make Dietary Changes?

The foods you eat create a solid foundation for your body to access plenty of essential nutrients for nourishment and restoration. Therefore, dietary changes are an integral piece of any recovery process from Lyme.

Salmon fish and avocado salad with fresh spinach leaves, broccoli, blueberry dressed with olive oil

And while there’s never a wrong time to make healthy changes, the sooner you begin to implement small adjustments, the quicker you’ll see results in gut-related issues like leaky gut and irritable bowel syndrome. You may notice some systemic changes as well, such as better energy, fewer symptoms of Lyme brain or brain fog, and a decrease in whole-body aches and pains.

But choosing the best nutrient-dense diet can sometimes be overwhelming. In reality, many foods market themselves as “health foods.” So how do you know what to pick to feed and care for your body adequately?

Generally, finding the healthiest selection of foods at your supermarket is as easy as shopping the perimeter of the store. That’s where the freshest items and the ones with the purest ingredients are located — think produce, lean meats, and healthy fats.

As you work to make changes, the majority of your diet should be plant-based foods, especially vegetables, says Dr. Rawls. That’s because vegetables contain nutrients to feed the beneficial flora of your gut, as well as fiber to help bind and vacate toxins.

Although you’ll want to nix foods with added sugar, low-sugar fruits like berries and apples offer an abundance of antioxidants and can help to curb your sweet tooth. You’ll also want to load up on healthy fats and proteins — foods like eggs, wild-caught salmon, chicken, olive oil, avocados, and ghee fit the bill.

If your intention is to get well (and we know it is), it only makes sense that you’d swap out the packaged, processed foods that generate inflammation or add to the toxic load that’s already burdening your body in favor of whole, nutrient-dense foods. If you pick up an item and don’t recognize or can’t pronounce the ingredients listed on the label, that product is better left on the shelf.

3. When Should I Begin Detoxing?

There are a variety of indications that it might be time to begin a detox routine, a main one being a Herxheimer reaction (herx for short). This worsening of symptoms occurs shortly after beginning a new treatment protocol as large quantities of pathogenic microbes are killed off, causing a flood of toxins throughout your body.

Green chlorella pills or green barley pills and powder in ceramic spoon.

When you’re in the midst of a herx, you’ll likely notice things like:

  • Worsening levels of fatigue
  • Disrupted sleep
  • Flu-like symptoms
  • Increased pain
  • Difficulty concentrating
  • Irritability
  • Headache

If you’ve treated chronic Lyme disease for a while, odds are you’ve already encountered a herx somewhere along the line. A herx is akin to a flashing neon sign alerting you that it’s time to lend a helping hand to your body and assist with the removal of dead bacteria and toxic byproducts.

If you need some detox ideas in a pinch, here are a few reliable go-to favorites among chronic Lyme patients:

  • Lemon water: Lemons stimulate the production of bile and help to cleanse your liver, which performs the vital task of detoxifying chemicals and metabolizing drugs. To experience benefits, add a splash of lemon to hot or cold water and sip away.
  • Milk thistle tea: Made by a variety of tea companies, milk thistle tea provides much-need liver support during a herx.
  • Activated charcoal: Typically available in a capsule or powder, activated charcoal is an affordable toxin binder that binds to a variety of toxins in the GI tract and helps you excrete them. “Most people do fine with charcoal, but it can cause constipation — which of course prevents toxins from exiting the body — so discontinue use if that happens for you,” says Dr. Rawls.
  • Chlorella: A freshwater green algae, nutrient-rich chlorella is made up of amino acids, iron, vitamins, and minerals. As a toxin binder, it works well for withdrawing heavy metals from your body.
  • Epsom salts baths: They’re a cost-effective way to decrease inflammation, lessen pain, and support liver and skin detoxification. The main component of Epsom salts is magnesium sulfate, a mineral known for its ability to calm the musculoskeletal and nervous systems.

It’s important to note that you don’t need to experience a herx to benefit from detoxification. Regularly practicing detoxifying behaviors — minimizing the inflow of environmental toxins, getting regular exercise (if possible), reducing stress, and getting ample sleep — wards off severe die-off reactions and helps you better tolerate your treatment protocol.

4. Should I Dive into the Full Dose of a New Protocol?

Because there’s no one-size-fits-all protocol, the way you incorporate natural therapies into your treatment protocol might be different from how someone else does it. While some people may be able to jump right away to full doses of an herb or supplement, others will have to work up slowly — both of which are perfectly fine.

single capsule on spoon. Yellow background.

Here are a few things to try, depending on your particular circumstances:

  • If you find that you need to lessen the pace a bit, try adding in a new herb or supplement every two or three days, as opposed to daily.
  • If you can’t tolerate a particular herb, or you experience an uncomfortable herx, back off for a while and consider detoxing or taking a break for a few days.
  • Try to resist the unspoken pressure that patients can sometimes feel when one person is moving through a protocol at a faster pace than others might be. What’s right for you is your best way to achieve recovery.
  • As you learn to listen to your body and work with it, you might find that as you get stronger, you’re able to increase your dosages or add in herbs that you couldn’t tolerate previously.

5. When is It Okay to Exercise?

When you have Lyme disease, exercise can be a tricky thing to figure out. You know you need to move, but if you do too much, you can set yourself up for a cycle of pushing, crashing, and flaring up. If you move too little, you lose muscle tone, strength, and stamina. So how do you find the delicate balance between doing too much and not enough?

“Exercise is beneficial,” says Dr. Rawls. “However, it’s equally as important to avoid overtaxing your body.” His rule of thumb? “Exercise as long as it feels good to you. If it ever results in a next-day ‘hangover’ with pain and worsening fatigue, you’ve pushed yourself too far, and you’ll need to allow yourself time to recover.”

Young woman doing pilates on mat in the park

When you’re ready to try again, dial down the intensity until you’re further along in your recovery. Swap out aggressive exercise with low-impact fitness programs like yoga, Pilates, qigong, or walking. As you begin to feel better, there’s a good chance you’ll naturally increase your activity levels without feeling like you’re draining your body of every last drop of energy.

Everybody experiences ups and downs as they recover. The key to a successful exercise program when you’re chronically ill is this: Be mindful of your limits and acknowledge that your body is healing at a speed that’s unique and right for you. Using a gentle, consistent approach to exercise, you’ll improve strength, endurance, and restore your body.

Above all, “Have fun,” says Dr. Rawls. “Make sure you’re engaging in activities that bring you joy and lessen your symptoms. That’s the best choice you can make for your health and well-being.”

6. How Long Will It Take to Work?

“It does take time,” says Dr. Rawls. Certain symptoms, particularly those found in people with neurological Lyme, can take months to years of steady, comprehensive herbal therapy to see substantial gains.

Doctor with alarm clock in hands

Although an herbal therapy approach tends to be slower, it’s important to remember that healing is cumulative. That’s because you’re chipping away at the underlying causes while simultaneously restoring health to your body — as opposed to only attacking microbes or masking the symptoms.

The good news is that because herbs have a low potential for toxicity, they can safely be used for a long time to suppress microbes, balance the microbiome, and establish a more robust immune system.

“It’s not a short-term proposition,” acknowledges Dr. Rawls. “It took me years of taking herbs to get my life back completely. And I’ve continued taking immune-supporting herbs long term — I think that’s really, really important for lasting wellness.”

Dr. Rawls is a physician who overcame Lyme disease through natural herbal therapy. You can learn more about Lyme disease in Dr. Rawls’ new best selling book, Unlocking Lyme.
You can also learn about Dr. Rawls’ personal journey in overcoming Lyme disease and fibromyalgia in his popular blog post, My Chronic Lyme Journey.


1. Melia MT, Auwaerter PG. Time for a Different Approach to Lyme Disease and Long-Term Symptoms. N Engl J Med. 2016; 374(13): 1277–1278. doi: 10.1056/NEJMe1502350
2. Chu L, Valencia IJ, Garvert DW, Montoya JG. Deconstructing post-exertional malaise in myalgic encephalomyelitis/ chronic fatigue syndrome: A patient-centered, cross-sectional survey. PLOS ONE. 2018 June 1. doi: 10.1371/journal.pone.0197811
3. Zellner T, Prasa D, Färber E, Hoffmann-Walbeck P, Genser D, Eyer F. The Use of Activated Charcoal to Treat Intoxications. Deutsches Ärzteblatt International. 2019 May; 116(18): 311–317. doi: 10.3238/arztebl.2019.0311