Prokinetics help prevent SIBO relapse by supporting gut motility, but they’re not a cure. Combined with hydrogen breath testing, tailored dietary plans, and practitioner-led care, they form part of a comprehensive strategy for lasting relief.

Managing Small Intestinal Bacterial Overgrowth (SIBO) can be challenging, especially when symptoms keep returning after treatment. One reason for relapse is impaired gut motility, which is when the small intestine doesn’t effectively clear food and bacteria between meals. This is where prokinetics can play an important role.

Prokinetics are medicines or supplements that support the natural muscle contractions of the digestive system, helping to keep bacteria from building up again. While they can be a valuable tool in a treatment plan, it’s important to understand that prokinetics alone won’t resolve the root causes of SIBO.

From a functional medicine perspective, they work best as part of a comprehensive approach that looks at your diet, gut health, and lifestyle to address the underlying issues driving bacterial overgrowth. For example, those affected by methane SIBO (overgrowth of methane-producing organisms) may like to take a look at dietary advice in our Methane SIBO Foods to Avoid guide.

What Are Prokinetics and How Do They Work?

Prokinetics are treatments designed to improve gut motility – the wave-like muscle contractions that move food and waste through the digestive system. In the context of SIBO, they help stimulate the migrating motor complex (MMC), a natural cleaning cycle that sweeps bacteria and food particles out of the small intestine in between meals.

When the MMC isn’t functioning properly, bacteria can remain in the small intestine and multiply, leading to symptoms such as bloating, gas, abdominal discomfort, and irregular bowel movements [1]. Prokinetics don’t kill bacteria directly, but by supporting this natural cleaning process, they reduce the likelihood of bacterial overgrowth returning after treatment [2].

The Role of Prokinetics in SIBO Treatment

Treating SIBO isn’t just about reducing bacterial overgrowth; it’s also about creating the right conditions in the gut to prevent the problem from returning. One of the most important factors in recurrence is gut motility. When the small intestine’s natural cleaning waves, known as the migrating motor complex (MMC), are impaired, food particles and bacteria can linger instead of being swept into the large intestine where they belong. This creates the perfect environment for bacteria to multiply again, even after a successful course of treatment [2].

Prokinetics help address this problem by stimulating the MMC and supporting the gut’s natural cleansing cycles. Their main role is therefore preventative. They are usually introduced after an initial treatment, such as antibiotics or herbal antimicrobials, has cleared the bacterial overgrowth. By improving gut motility, they help reduce the risk of relapse [2], which is one of the most common challenges for people with SIBO.

However, it’s important to understand that prokinetics are not a cure. On their own, they won’t eliminate bacterial overgrowth or address why it developed in the first place. That’s why, in functional medicine, prokinetics are seen as a tool rather than a standalone solution. They work best as part of a comprehensive plan that also investigates and treats the root causes, be that low stomach acid, a disrupted gut microbiome, food intolerances, or stress-related gut dysfunction.

Used in this way, prokinetics can help create the stability needed for long-term healing. They don’t just reduce the risk of SIBO returning, but also support better digestion, more regular bowel habits, and improved quality of life when combined with personalised nutrition and lifestyle strategies.

Prescription vs Natural Prokinetics

Common prescription options and their uses

In clinical practice, several prescription medications are sometimes used as prokinetics to support gut motility in patients with SIBO:

Low-dose erythromycin – An antibiotic used not for its antibacterial effect but for its ability to stimulate the migrating motor complex [3]. Often taken at bedtime to encourage overnight gut cleansing.
Prucalopride – A 5-HT4 receptor agonist that promotes intestinal contractions. It’s sometimes used in cases where constipation and slow motility are significant contributors to SIBO [4].

These medications can be effective, but they are generally prescribed under medical supervision, particularly because of the risk of side effects or interactions with other treatments.

Natural prokinetic alternatives in functional medicine

For those seeking a more holistic approach, natural prokinetics may be considered. These can be gentler while still providing support for gut motility:

Ginger – Widely used in functional medicine for its ability to stimulate digestion and enhance motility.
Iberogast – A herbal liquid formula combining extracts from several plants, used to support gut motility and reduce bloating.
Low-dose naltrexone (LDN) – Though not strictly “natural,” it is sometimes used in functional medicine at very low doses to support motility and reduce inflammation.
5-HTP – A supplement that supports serotonin production, which plays a role in gut motility.

These options are often combined with dietary and lifestyle interventions, with the choice tailored to the patient’s unique health profile. A functional medicine practitioner can help determine which approach is best suited to an individual’s needs.

Why Prokinetics Alone Are Not Enough

The importance of addressing the root cause of SIBO

While prokinetics can play a valuable role in reducing the risk of relapse, they don’t tackle the underlying reasons why SIBO developed in the first place. Small intestinal bacterial overgrowth can occur for various reasons, such as low stomach acid or use of certain medications such as antibiotics [5], to complications of abdominal surgery, structural problems in the small intestine (scars or adhesions), and certain medical conditions that slow the transit of the gut, including Crohn’s disease and diabetes [6]. If the root causes are not identified and treated, symptoms are likely to return, even if prokinetics temporarily improve motility [5].

A functional medicine approach goes beyond symptom management, aiming to uncover and address the drivers of SIBO through thorough history-taking, testing, and personalised care. Prokinetics, in this context, are one tool in a broader strategy rather than a standalone solution.

Risks of relying on symptom management without full treatment

Using prokinetics in isolation risks creating a cycle of partial relief without lasting results. Patients may find that while bloating and discomfort improve for a time, symptoms eventually return as the underlying imbalance remains untreated. In some cases, relying only on symptom management can delay a proper diagnosis of contributing factors such as food intolerances, thyroid dysfunction, or chronic stress, allowing these issues to persist or worsen.

For meaningful and long-term improvement, prokinetics need to be integrated into a comprehensive treatment plan that addresses diet, lifestyle, gut health, and any contributing medical conditions.

A Functional Medicine Approach to SIBO

Testing to identify underlying triggers

A functional medicine approach looks beyond symptom control to uncover why SIBO has developed and why it may be recurring. This often includes hydrogen breath testing – a simple and non-invasive testing method you can do at home – alongside a detailed health history to explore factors such as diet, gut microbiome balance, stress, and digestive function. Identifying these root causes ensures treatment is targeted, rather than relying on trial and error.

Combining tailored support with practical strategies

Treatment typically combines a number of elements: dietary changes matched to your individual needs, lifestyle adjustments to support digestion, and where appropriate, the use of prokinetics to prevent relapse [5]. Regular support sessions with a practitioner help guide you through the process, adapting your plan as your symptoms improve and your gut health strengthens.

Personalised care plans for lasting results

At IBS Clinics, we take this functional medicine approach a step further through our I Can Beat SIBO programme – a six-module, practitioner-led online course designed specifically for women.

What makes it unique is its combination of structured learning with personalised, practical tools: tailored dietary plans for different SIBO types, hormone-aware symptom tracking, and at-home testing guidance for stomach acid and digestive function. Unlike generic advice, the course is designed by experienced practitioners and provides resources you can put into action straight away.

This blend of professional expertise, evidence-based strategies, and practical tools helps patients not just to manage symptoms but to address the underlying causes of SIBO, supporting long-term digestive health and wellbeing.

When to Consider Prokinetics as Part of Your Plan

Prokinetics are not suitable for everyone with SIBO, but they can be particularly helpful if you’ve noticed symptoms returning soon after treatment or if you have a history of slow gut motility. Common signs that prokinetic support may be appropriate include persistent bloating, discomfort that worsens after meals, irregular bowel movements, or a pattern of recurring SIBO despite previous treatment.

Working with a practitioner to find the right option for you

Because prokinetics are most effective as part of a wider functional medicine plan, it’s important to use them under professional guidance. A practitioner can help identify whether a prescription or natural option is most appropriate, ensure it’s safe alongside your other treatments, and integrate it with dietary and lifestyle strategies tailored to your needs. This personalised approach helps you get the best results while addressing the root causes of SIBO, not just the symptoms.

Conclusion

SIBO can be a stubborn and recurring condition, especially when gut motility issues play a role. While prokinetics are a valuable tool in preventing relapse, lasting relief comes from a more comprehensive approach. Accurate testing, personalised dietary changes, and practitioner-led support are essential to addressing the root causes and restoring healthy gut function.

At IBS Clinics, we combine evidence-based testing, including hydrogen breath testing, with personalised advice to create treatment plans that are both practical and effective, while our I Can Beat SIBO course is a unique option for women seeking structured support.

If you’re ready to move beyond temporary fixes and take a structured approach to recovery, our practitioners are here to help. Contact us at IBS Clinics today to learn more about testing, tailored care, and how the I Can Beat SIBO course can support your journey to long-term relief.

References

https://pubmed.ncbi.nlm.nih.gov/22450306/
https://www.sciencedirect.com/science/article/abs/pii/S089990072400114X
https://www.nice.org.uk/advice/esuom13/resources/erythromycin-for-gastroparesis-delayed-stomach-emptying-pdf-17474679493
https://www.mayoclinic.org/drugs-supplements/prucalopride-oral-route/description/drg-20452343
https://my.clevelandclinic.org/health/diseases/21820-small-intestinal-bacterial-overgrowth-sibo
https://www.mayoclinic.org/diseases-conditions/small-intestinal-bacterial-overgrowth/symptoms-causes/syc-20370168

Author – Tracey Randell

At IBS Clinics, Tracey Randell, a renowned Nutritional Therapist and one of the few IFM Certified Practitioners in the UK, extends her specialised knowledge and unique approach to managing and treating IBS and other gut-related conditions effectively.

Tracey’s profound understanding of Functional Medicine allows her to connect the dots for complex health conditions, identifying and addressing the root causes to curate personalised and comprehensive health plans for her patients. Her holistic approach focuses on resolving underlying imbalances and optimising gut health, enabling the body to correct other issues and attain overall well-being.

At IBS Clinics, we are dedicated to being your partner in navigating your gut-related health concerns, offering expert care and individualised treatment plans to alleviate your IBS symptoms and enhance your quality of life.

DISCLAIMER: The information provided in this article is intended for general informational purposes only and should not be construed as medical advice, diagnosis, or treatment. The products and methods mentioned are not a substitute for professional medical advice from a trained healthcare specialist. Always seek the guidance of your doctor or other qualified health professional with any questions you may have regarding your health or a medical condition. Never disregard professional medical advice or delay in seeking it because of something you have read on this website. Use of the information and products discussed is at your own risk.