My experience taking antibiotics for chronic Lyme disease. Click to read or pin to save for later.
Photography credit:
This post contains affiliate links. Click here to read my full disclosure policy.

Taking antibiotics for acute Lyme disease (early infection) is a given. But, the water becomes more muddied when it comes to taking antibiotics for late stage Lyme disease, otherwise known as chronic Lyme disease.

Some suggest antibiotics are required in combination and need to be pulsed for long periods of time. Others say there is no scientific literature to support the use of long-term antibiotics and alternative approaches are more beneficial.

Whichever camp you are sitting in, know that I appreciate there is no one path to remission from chronic Lyme disease. Everyone is individual and that path will have unique factors for each person.

As a person with chronic Lyme disease, you need to follow your gut and choose the treatments that feel right to you. That’s all we can do and it’s the approach I personally take.

A relapse in symptoms that led to antibiotics

You may recall that I had a relapse of Lyme disease symptoms back in January. On speaking with my doctor from Breakspear Medical, he decided the best course of action was to prescribe antibiotics. I had never taken antibiotics before and thus far had been using herbal therapies, supplements and artesunate.

I, therefore, wondered if taking a course of antibiotics was something I needed to do to get me over my latest setback. What if they were what I needed to progress forward in my recovery? I was open to the idea and decided it was worth trying.

From my symptoms, my doctor also diagnosed Bartonella. I was therefore put on two different types of antibiotics. One to treat the Lyme spirochetes and another to tackle the cyst form of Lyme and also Bartonella.

I was also given biofilm breakers and supplements for gut, liver and mitochondrial support. I also continued with detox supplements, as well as continuing to use my far infrared sauna on a regular basis.

My experience with antibiotics for chronic Lyme disease

All of this sounded like a decent plan to me and I took these antibiotics for six weeks. I was meant to take them for longer but, following my gut feeling, I decided six weeks was all I wanted to do. You’ll understand why by the time you reach the end of this blog post.

I am going to share my experience with these particular antibiotics. Again, before I begin, I want to stress that this is my personal story. Others may have a completely different experience to me.

I just believe in being honest about my own experiences on my blog and I don’t shy away from talking about things that have been difficult for me.

As I mentioned at the beginning, there is no one way to treat chronic Lyme disease and its associated co-infections. You have to do with is right for you, as I have to do what is right for me.

With that all said, here are a few things I learned about taking antibiotics for chronic Lyme disease:

1. The herxing was much worse than I experienced with herbal therapies

A herx reaction, formally known as a Herxheimer Reaction, is an increase in symptoms caused by the release of toxins as bacteria die. It causes all of your usual symptoms to worsen.

When I started herbal therapies, I herxed. It lasted a short time and then my symptoms resided and I gradually began to feel better overall.

With the antibiotics, the herx I experienced was much worse. For me, it meant feeling even more flu-like, incredibly fatigued, I was in more pain (my neck pain was excruciating at times), and my sleep was awful.

I struggled to fall asleep and it became very, very disruptive. This, of course, would not be helping things.

2. The herxing lasted longer than I expected

To combat the effects of herxing, you need to support your body’s natural detox pathways. If you are adding to the burden, you need to assist your body in getting rid of these extra toxins.

For me, this included: using a far infrared sauna on a near daily basis; Epsom salts baths, drinking more water than usual (often lemon water); supplements such as liposomal glutathione, liposomal vitamin C and alpha lipoic acid, herbs such as Burbur (which is great!).

Despite this, I felt as though I was in a herx the majority of the time. I didn’t want to do too much of a good thing but I felt as though I was doing a good job of supporting my body.

It didn’t seem to be enough though and I suffered each day. It was a much different experience for me compared to herbal therapies.

3. The side-effects can be horrible

If herxing wasn’t bad enough, I also suffered from unpleasant side effects from the antibiotics. I was nauseous 24/7. My appetite completely tanked and I could only stomach certain foods (puffed rice cereal was my saviour). When I did force myself to eat something, it was only small amounts.

The ironic thing was that eating helped to relieve my nausea but I couldn’t stomach eating. It was horrible. I tried many things to help ease it, such as copious amounts of ginger tea, but nothing took it away completely.

I also got banging headaches, though I’m unsure if this was a side effect or a symptom of herxing.

4. I struggled mentally

One of the worst aspects for me was how all of this affected my mental health. I had zero motivation throughout the time I took antibiotics (and I still have low motivation a few weeks later). I didn’t want to blog and I didn’t want to do much of anything.

Each day I felt incredibly fed up with feeling so awful. At times, I just wanted to cry at my own misery. It was so strange to be aware of this and not want to be like that, but have zero control over it.

5. My level of functioning decreased

I have had energy issues for years. It is my biggest problem. No matter how well I feel, I am restricted in how much I can do. When I added antibiotics into the mix, things got even worse. My level of functioning tanked.

I physically did very little during those six weeks. I spent the majority of my time resigned to the sofa. I couldn’t bring myself to go back to bed but I probably should have on some days.

I lived in fear that I was poisoning my mitochondria and, who knows, maybe I was. My energy has only slightly improved since stopping the antibiotics. I still struggle with things that were no longer an issue before, such as climbing the stairs.

6. I am stronger than I know and I never let go of hope

All of the above sounds pretty awful, doesn’t it? And it absolutely was. Regardless, I still took those pills religiously.

The reason was that I never let go of the hope that they were going to help me. It did reach the point where I felt the duration I had taken them was sufficient.

I could only do it to myself for so long and didn’t want to put myself through it anymore. But, I made sure I endured them for long enough so that I could see if they had helped or not.

7. The antibiotics did help

When I stopped taking the antibiotics, I felt better than I did during my relapse back in January. However, the improvement was not significant enough for me to want to continue with them.

My thought was, they had gotten me past my relapse but that I wanted to go back to herbs moving forward.

Luckily, without me even saying, my doctor came up with the same plan. So I am back on a herbal regime, along with artesunate, for the foreseeable future.

My doctor has also done some further testing, which I’ll talk more about in a future post. I have had one result back that I’ll talk about now as I feel it fits in with this topic.

8. Antibiotics can wreak havoc on the gut

I never had many symptoms of gut problems during the time I took antibiotics. I took probiotics, which everyone should take with antibiotics (along with maintaining a sugar-free diet), and I hoped the damage would be minimal. I also took Lauricidin.

However, I had a test recently, which showed I have pretty high levels of candida. I know from previous testing that I had a mild yeast infection before (though nothing of much concern). But now the antibiotics have left me with a real problem with candida.

I know this post hasn’t been particularly positive but I thought it was worth being honest and sharing my experience. I think we all have different tolerances for medications and my body doesn’t seem to like antibiotics.

I believe it was one antibiotic, in particular, that was a big problem for me. I did consider trying a different type but in the end, I am glad that my doctor decided that I should go back to herbal therapies.

Let me know your thoughts in the comments. Have you taken antibiotics for chronic Lyme disease? Was your experience similar to mine? Or have you had a better time of things?

Pin for later:

My experience taking antibiotics for chronic Lyme disease. Click to read or pin to save for later.


Hello, I'm Donna. I was diagnosed with Fibromyalgia in 2013 and started this blog shortly after. After my health declined significantly the following year, I decided to become my own advocate and searched for answers. It took two years but, in 2016, I finally discovered I had Lyme Disease. On February Stars, I share my personal journey back to better health; discussing what has helped me and the mistakes I've made along the way. I also cover topics on self-improvement, managing symptoms and living life to the fullest with chronic illness.


  1. Taking antibiotics for Lyme nearly killed me, and yet I always felt better afterwords. Eventually they killed my gut so much I had to off, but since then I’ve been on IV antibiotics for other things and it’s amazing how much better I feel afterword. Good luck to you as you continue Lyme treatment!

    • They are so tough, aren’t they? The benefit wasn’t enough for me to want to continue at the moment and I’m looking into other things. It’s great you have felt the benefits from them. But I know what you mean about wreaking your gut. I just learned that I’ve got a bad candida infection and though my doctor says it’s been chronic and the antibiotics won’t have had too much to do with it, I can’t help but think they did. Thanks!

  2. Oh my word, I can identify with this SO much! I am on antibiotics for Lyme right now after several months break and it is literally killing me. I can hardly move because of the fatigue. The nausea is totally ridiculous and the pain levels are even worse. Sending you healing thoughts and gentle hugs as you continue with your treatments. xo

    • It’s nice to know it’s not just me who has struggled (as much as I wish you weren’t). The fatigue is just the worst, isn’t it? Oh and the nausea and pain… it makes me sick thinking of it! I hope you see improvements with treatment and I wish you all the best

  3. Annalisa Walker Reply

    I was diagnosed with Lyme in 2011. I was on antibiotics from December 2011- March 2017. I was probably on at least 10 different ones off an so on. Maybe even more. I did intra-muscular shots of Rocephin for a year also. I definitely believe the antibiotics helped save my life. I went from being basically bedridden and not knowing my kids names to working full time again after a year of being on them.

    With that being said, I had never gotten completely better. And then in March 2017 I was feeling miserable – like I had a flu bug – different from lyme stuff. They ran bloodwork and found my WBC to be 1.7 and I was not producing any bone marrow. I felt horrible! So I was taken off the antibiotic that I had been on for pretty much the whole five years. This was a side effect that could happen if taking it long term that I was unaware of.

    I recovered from that and actually felt perfect and lyme free once that situation was resolved. I went on my merry way thinking I was healed!

    However, in June of this year I had a pretty bad neuro setback – memory, numbness in face, anxiety, panic attacks, basically feeling horrible, heart issues.
    This started after leaving Target. My LLMD says the lights triggered the attack.
    So…I started back up hard on ALL of my supplements and herbals. It took until July 6 to start feeling better again.

    My LLMD doesn’t want to start back on antibiotics. He believes in treating your whole self. So I am going to a brain retraining conference this fall to help with my maladaptive wiring and synapses that have been created while dealing with chronic Lyme.

    I want to say that the whole time I was on antibiotics I was also on herbals. So I hit it from all angles. I also have a good detox protocol.

    My overall journey has been long and difficult, but also have grown and changed in ways I ever would have. I am so thankful for my LLMD and naturopath, who I know saved my life.

    As far as long term antibiotics…I am lucky i never developed any stomach/gut issues the entire time I was on them. I think they saved my life. But they definitely did not cure Lyme. They did help me get back to living again however!

    I will stick to my herbals and supplements, work on healing my brain, and take it a day at a time. The herbals i take are for lyme, Bartonella, and Babesia. I use products from a few different companies and feel lucky to have had the guidance from my doctors to know which ones help me the most.

    I’m glad I found your post today! I wish you well and Healing!

    • Hi Annalisa

      I feel that antibiotics absolutely have their place and I think that there is no one road to healing. It’s great that you have been helped so much by antibiotics. They really work wonders for some people and, as you say, can be life saving.

      Lyme is so complicated isn’t it? There are
      so many facets to it and many paths to take. That’s why i wanted to stress that I don’t believe there is a right or a wrong way to treat it. If I had felt more of a benefit from abx I would have definitely continued with them. But it was hellish for me and I guess because I was taking herbals before that I had a comparison there. And my improvements and quality of life are definitely better on herbals vs antibiotics.

      However, that is a very personal thing
      We are all individual and I would never discourage anyone from trying a treatment. It’s more that I wanted to share how I was getting on because people have been following my story and I couldn’t be dishonest about my experience.

      Your doctor sounds great and it looks like he appreciates the impact Lyme & co can have on all the different systems of the body.

      Thank you for your comment. I wish you well in your healing and hope you continue to see improvements ????

  4. I’m on my second round of antibiotics and I’m living what you went through. The herxing is like living with coming down with the flue everyday. I never feel well. I have broke into tears. I take tons of the right supplements, bodywork, bemer matt and I’m a sick person.

    I took 6 weeks of Doxy and azithromycin, now this is my second week on the 2 Bartenella antibiotics. I have to stop I have to work. I need a break.

    I think I have had Lyme a long time, 15 years. A lot of symptoms are so much better but I’m sick. I’m going to take the weekend off and then look at it again. I have to be able to work, not an option.

    Thanks for your blog. It cut through my isolation of doing this by myself. My plan is to continue to treat herbally at the end of the abx treatment.

    This may be sooner that I thought.

    • Hi, Cindy. I am sorry to hear you are having such a rough time with the antibiotics. I remember it well. To put it bluntly, I found it pretty hellish! I was on antibiotics for Bartonella too– they were what gave me the most problems. I gave up after 6 weeks if I remember correctly. My doctor wanted me to take them for 3 months but there was no way I could do that. I went back on to herbal therapies and then at the end of last year I took a leap of faith and had treatment at Infusio (stem cells). My experience has shown me that there are other options than antibiotics that work and help. We will all walk a different path and there’s no right or wrong treatment. It has to be what’s best for each of us as an individual. Have you read the book Unlocking Lyme by Dr Bill Rawls? I found that a really helpful and insightful read.

      • Jenny Kirkpatrick Reply

        Hi Donna, I’ve been undergoing treatment for Lyme for over three years.. my dr believes I’ve had it since childhood. I’m interested in your stem cell treatment and you’re results of you don’t mind sharing with me. I live in Texas and my dr just mentioned to me about this treatment coming to Houston Texas and being a possibility for me. It is very expensive and I’ve not seen much on the pros and cons of the stem cell treatment. I appreciate any response. God bless you and pray for healing for us all.

        • Hi Jenny, I have blogged all about my stem cell treatment from my experience at the clinic with updates through until now (which I will continue to add to). You can find all of my posts about it here. I would encourage you to do as much research as possible as there are different treatments available. I decided on treatment at Infusio as I wanted autologous stem cells (ie. from my own body) for safety reasons. I also believed their pre-treatments were important to prepare the body for stem cells. Good luck and I hope you find a treatment that works well for you.

  5. Thank you for your quick response. I’ll get the book.
    I’m finding my way….I went untreated for over 15 years. My tests came back negative. My doctor wouldn’t treat me because my tests came back negative. I don’t think he cares about me. Time for a new doctor.

    The 1st round of antibiotics wiped out 15 years of migraines and a bunch of other painful symptoms. I hope they don’t come back. I hope I recover from the antibiotics.

    The journey continues….

    Thanks again!

    • It’s so unfair how Lyme patients are often treated by doctors. I had to work through a lot of different emotions when I finally learned I had Lyme. It’s not easy coming to terms with the devastation it causes, knowing that it’s a disease that can be successfully treated in the early stages. I truly hope the benefits you have found from the antibiotics continue and your symptoms do not return. You will bounce back from the antibiotics. It took me a good few weeks (and I also went back on to herbals which no doubt helped) but I got there and found my way forward again. Good luck!

  6. I’m from California I have had Lyme for 1 year to date while visiting Florida. which I was not aware of what I was looking at but it was in fact a engorged tick in my ankle that itched so bad! I fell asleep and it was gone by the morning. I had no way of knowing As I am uneducated never knew much about ticks. To close my eyes and see the tick in me makes my stomach sick or anytime I see a tick engorged it sends extreme anxiety to me. Doctors are not helping. I insisted to be texted and came back positive for Lyme igg With Co infections Mono I still believe some co infections was missed. I was given 3 weeks of antibiotics and insisted on a additional week. My symptoms was and still is extreme tingling of the hands and feet. Symptoms went away and recently came back and I’m faced with starting antibiotics again or herbal . I believe I ordered so many different herbal meds and I’m self medicating because the doctors say I’m fine but I feel
    My body will never return to normal. I wonder is the symptoms means a spirochete is getting killed or if that means they are thriving ? How do you know ? I have brain fog and feel my memory is so terrible. My knees & armes feel twitching sometimes but inflammation is much better. Impaired to 1 year ago. I started taking doxy because I had some left but I experienced some side effects ie herxing with diarrhea and throwing up . Also I was told that itching was a sign of Candida so I am now trying to treat that. Don’t mean
    To ramble but there is so much I’m leaving out and so much more to say. By for now sending well wishes to all

    • I’m so sorry to hear you have Lyme Disease. I too was very ignorant about ticks but I never even saw the one that bit me. There definitely needs to be better education about the dangers of tick bites. I can also appreciate the fear and anxiety around ticks. I am so anxious about any biting insect now. It’s so hard to get appropriate treatment when many health professionals don’t believe that Lyme can be a chronic illness. This resource may be helpful for you in deciding whether you are herxing or if it is something else. I’d also recommend reading a book called Unlocking Lyme by Dr Bill Rawls. You can find my review of the book here. It’s full of really helpful information that may help you to make better sense of everything.

  7. I was on antibiotics for my first six months of lyme treatment, took a break and now that I’m back on them after trying to rebuild my gut I feel like I’m not getting anywhere. My stomach hurts so bad it feels like knives stabbing me any time i eat anything. I’m not sure what to do or how much longer I can continue before having to just flat out stop eating or stop antibiotics.

Write A Comment

This site uses Akismet to reduce spam. Learn how your comment data is processed.