Why Does My SIBO Keep Coming Back?
You’ve done the low FODMAP diet. You’ve taken the supplements. Maybe even done multiple rounds of antibiotics - So why does your SIBO keep coming back?
You get a few weeks (maybe months) of relief, but then the bloating creeps back in. Constipation or loose stools return. Your energy crashes. The brain fog follows. And you're left wondering if this cycle will ever actually end.
Here’s the truth: If your SIBO keeps coming back, you haven’t found the real root cause. And until you do, the symptom-chasing will never stop.
Let’s dive into the real root cause of SIBO and how to end the vicious cycle once and for all.
Many people are told they have SIBO (small intestinal bacterial overgrowth) and are sent down a path of repeated antibiotics or herbal antimicrobials. While these may offer short-term relief, they often don’t address the why-why the overgrowth happened in the first place, and why it keeps coming back.
If you’ve felt like you’re just managing symptoms without making real progress, it’s because the deeper root causes haven’t been fully supported. That’s where root-cause work comes in.
We need to look beyond just killing bacteria to investigate what allowed that overgrowth to occur in the first place:
Breakdown in the gut’s self-cleaning mechanisms
Environmental mold exposure and fungal overgrowth
Nervous system dysregulation, mineral depletion & slowed motility
Because real healing isn’t just about killing bacteria, it’s about rebuilding a resilient and optimally functioning digestive system that operates efficiently on its own.
The Real Root of SIBO
What is SIBO?
SIBO happens when bacteria, even the normal kind, overgrow in the wrong place, your small intestine. When these bacteria start to ferment your food, they create gas and byproducts that lead to inflammation and symptoms like:
Persistent bloating (especially after meals and worse at night)
Abdominal pain or cramping
Belching or excess gas
Constipation, diarrhea, or both!
Fatigue and brain fog
Food sensitivities
Skin flare-ups, especially rosacea
Most protocols are focused on killing the bacteria with antibiotics like rifaximin or herbal antimicrobials. And while this might bring short-term relief, it often doesn’t address the root issue. Killing bacteria over and over without improving motility, restoring digestive flow, or rebuilding the gut environment is like cutting weeds without pulling up the roots; it will keep coming back. In fact, repeated antibiotic use can weaken the microbiome and make you even more vulnerable to future overgrowth.
That’s where our root cause approach is so essential for successfully treating SIBO, so it doesn’t come back!
We partner with our clients to investigate their unique root cause using comprehensive functional labs, personalized nutrition, and targeted supplements to rebuild resilience from the inside out!
Let’s explore the most common deeper root causes we see in practice with recurring SIBO.
Why SIBO Keeps Coming Back
Breakdown in the Gut’s Self-Cleaning Mechanisms
One of the most overlooked reasons for recurring SIBO is a breakdown in the self-cleaning mechanisms of the gut from impaired detoxification, sluggish bile flow, and slow gut motility.
Your liver and gallbladder play a critical role in what we think of as the gut’s self-cleaning mechanism. The liver filters toxins and produces bile, while the gallbladder stores and releases that bile into the small intestine. Bile is often only associated with fat digestion, but it also acts as a natural antimicrobial that helps prevent bacteria and yeast from overgrowing where they don’t belong.
When bile flow becomes congested or slow, the body’s innate antimicrobial protection weakens. On functional stool testing that we run with our 1:1 clients, this can show up as elevated fat markers, low pancreatic elastase, or signs of malabsorption. That clues us in that the gut isn’t clearing out waste efficiently, which can lead to the persistent overgrowth of SIBO, and these are markers we often see impaired in our chronic SIBO clients.
Bile is also a motility driver in the gut and a major part of our detoxification system that takes out the trash from the greater body. When bile flow and gallbladder issues are present, this can lead to the body struggling to eliminate not only stool but also toxins, excess hormones, and can drive inflammation in the greater body, leading to common SIBO symptoms like:
Persistent bloating or heaviness that makes you feel uncomfortable in your clothes
Lingering gas or burping
Low energy or brain fog, as SIBO impacts more than just your gut
Incomplete bowel movements, where you never feel truly relieved
This is where functional testing is crucial to determine which areas of the gut’s self-cleaning mechanisms need support to truly address why SIBO is there in the first place. It’s not just about killing off bacteria; it’s about creating an environment where overgrowth can't keep returning. When we support the full picture, we give the body what it needs to heal long-term.
What Your SIBO Protocol Missed
Nervous System Dysregulation, Mineral Depletion, and Slowed Motility
If you’ve done all the “right” things for SIBO - killing protocols with antibiotics or antimicrobials, low FODMAP diets, fasting protocols - and you still feel stuck. You’re not broken - you’re depleted. True healing starts when we focus on resilience, not just removal.
Lasting gut healing depends on more than just killing bacteria. It requires a strong foundation, and that comes from nourishing your body to repair nervous system regulation, replete mineral status, and restore optimal motility. These three layers of foundational support work to repair your resilience, which helps to keep digestion, motility, detox pathways, and immune function running smoothly so that the body can protect against SIBO all on its own.
Nervous System Regulation
Chronic stress doesn’t just make you feel on edge - it puts your entire body in survival mode. When the nervous system is stuck in fight-or-flight, digestion slows down, motility stalls, and your gut’s natural defense systems take a back seat. Over time, this creates the perfect environment for bacterial overgrowth to return. Even if you’re eating all the right foods or doing SIBO protocols by the book, your gut can’t fully heal if your nervous system is still signaling danger. Until your body feels safe, it won’t prioritize digestion, detox, or repair, which is why nervous system support is non-negotiable in breaking the cycle of chronic SIBO relapse.Mineral Balance
When it comes to healing chronic, recurring SIBO, most people focus on what to remove, but what’s often missing is what the body needs more of to function properly. And one of the most powerful, overlooked tools is minerals like sodium, potassium, magnesium, and calcium. These are the raw materials your cells need to run every process tied to digestion, motility, and nervous system function. If you're depleted, often due to stress, restrictive diets, medications, or poor gut absorption, these critical functions slow down or break down altogether. Low minerals mean poor motility, weak stomach acid, sluggish bile, and a nervous system that stays stuck in survival mode. That’s the perfect setup for SIBO to keep coming back.This is why our approach shifts the focus from “killing off bacteria” to replenishing what your body is missing - because true resilience comes from restoring function, not just reducing symptoms. It's not about cutting more out, it’s about giving your body the tools it needs to protect itself and finally break the cycle.
Slowed Motility
One of the most overlooked drivers of chronic SIBO relapse is slowed gut motility - specifically, a sluggish migrating motor complex (MMC). Think of the MMC as your gut’s “cleanup crew.” Between meals, it sends wave-like contractions through the small intestine to sweep out bacteria, food particles, and waste. But here’s the problem: when the MMC isn’t working well, often due to stress, nervous system dysfunction, mineral depletion, or eating too frequently, things get stuck. Bacteria that should have moved out start to build up, creating the perfect storm for SIBO to return again and again. This is why supporting motility is one of the most essential but under-addressed steps in true, lasting gut healing. If you’re stuck in the cycle of low-FODMAP diets, antimicrobials, and temporary relief… this might be the missing piece your gut has been waiting for.
Our approach is to rebuild the foundations that keep your body resilient. We support clients holistically using key nutrition strategies, lifestyle tools, and targeted supplements to rebuild the body’s resilience from the inside out.
True healing happens when the body feels safe, supported, and strong!
SIBO Relief That Lasts
The Hidden SIBO Driver: Environmental Mold Exposure & Fungal Overgrowth
The final hidden root cause we see as a driver in chronic, recurring SIBO is environmental mold exposure and small intestinal fungal overgrowth (SIFO).
Mold is sneaky. You can be exposed to mold without even realizing it by living or staying in a water-damaged building. It might be your home, but it could also be staying in hotel rooms with poor ventilation, musty vacation rentals, or older buildings with hidden damage behind walls, in basements, or beneath carpets and behind kitchens. You don’t always need to see or smell it for it to be affecting your health.
Mold spores can colonize in the sinuses, lungs, or gut and release mycotoxins - harmful compounds that can damage your gut lining, suppress your immune system, hijack your nervous system, deplete your minerals, and overwhelm your detox pathways. Mycotoxins are a powerful root cause that disrupts the gut’s self-cleaning and defense systems, like motility, enzyme output, and immune regulation, setting the stage for SIBO to develop. Until mold toxicity is addressed, SIBO will continue to return no matter how perfect your protocol is.
If we suspect a chronic SIBO client is struggling with mold exposure, we run a urine mycotoxin test to test the client's body before we start looking for the place of exposure. So often, we see positive mycotoxin tests showing up in our clients who have treated SIBO multiple times, but it continues to keep coming back. It is because mold is the root cause that leads to the bacteria colonizing the small intestines.
If we suspect mold is part of the picture, our approach goes beyond just treating symptoms. We work to identify hidden exposures, support the body’s ability to clear toxins, and repair the damage mold can leave behind. Unless mold is addressed first, it will be challenging for the gut to fully heal and for SIBO to be cleared long-term.
Here are the symptoms of mold and fungal exposure, if you suspect this might be part of your SIBO story:
Brain fog or trouble concentrating
Chronic fatigue or energy crashes
Bloating and gut issues that won’t go away
Sinus congestion, post-nasal drip, or frequent sinus infections
Anxiety, mood swings, or depression
Skin rashes, itching, or hives
Tinnitus, vertigo, or POTs
Ear infections or a history of ear infections
Recurring yeast infections or thrush
Chemical or fragrance sensitivity
Sleep disturbances or night sweats
SIBO or Candida that keeps coming back
If mold or fungal overgrowth is part of your story, it’s not just about clearing bacteria—it’s about restoring balance at a deeper level. When we address the real root causes, the gut finally has the chance to heal fully and stay that way. You don’t have to keep cycling through the same protocols. There is a way forward—and it starts with understanding what’s actually at play.
Stop Chasing SIBO Symptoms
Recurring SIBO Client Case: When 10 Rounds of Antibiotics Didn’t Work
After working with another provider and completing 10 rounds of antibiotics, this client was still stuck in a relentless cycle of SIBO relapse. He came to us with chronic loose stools, multiple incomplete BMs daily, deep fatigue, body aches, brain fog, and poor sleep that left him feeling drained every morning.
Testing revealed that his gut’s self-cleaning systems were severely compromised: sluggish bile flow, extremely low digestive enzymes and stomach acid, detox pathways that were clogged and overwhelmed, and signs of immune overactivation. No matter how many times the bacteria were "killed," his gut couldn't maintain balance.
After one relapse in our care, we knew we were missing part of the story, and ran a urine mycotoxin test. It came back positive. Mold was the missing piece that explained the breakdown in his gut’s ability to self-clean and why he was struggling with chronic recurring SIBO.
With that insight, we were able to get highly targeted with his protocol, supporting his body’s ability to clear toxins, repair damage, and rebuild its gut-cleansing rhythm. Today, he’s SIBO-free, energized, clear-headed, and has strong, complete daily BMs.
Sometimes it’s not about doing more - it’s about finding what’s been driving it all along.
Tired of treating SIBO over and over without real results?
If you're stuck in the cycle of bloating, food sensitivities, fatigue, and gut issues that keep coming back, it’s time to dig deeper. This is where working with a practitioner 1:1 who understands how all of these systems are connected and who can create a customized protocol unique to you can make all the difference.
Book a free strategy call and let’s uncover what’s driving your symptoms - so you can finally break the cycle and feel like yourself again.
Related Posts: Antibiotics and Low-FODMAP diets are not treating your SIBO!
