The Best Prokinetics to use for SIBO, IBS and Functional Dyspepsia (and when to use them)
- thegutremedy
- Jan 6
- 8 min read
If you’ve been dealing with SIBO, IBS or Functional Dyspepsia for a while, you’ll probably have come across the idea of gut motility - and specifically the migrating motor complex (MMC).
I’ve written in more depth about this here, but in short, the MMC is the housekeeping wave that clears leftover food and bacteria from the small intestine between meals. When it isn’t working well, symptoms like bloating, pain, reflux, nausea and relapse after treatment become much more likely.
This is why prokinetics often come up in conversations about stubborn or recurrent gut symptoms. They don’t kill bacteria or suppress symptoms. They support gut movement, and for many people, that's the missing piece.
What are prokinetics?
Prokinetics are substances that support coordinated gut movement, particularly the migrating motor complex, which helps clear the small intestine between meals [1] [2].
They may:
Stimulate the MMC
Improve stomach emptying
Support small intestinal clearance
Improve communication between the gut and nervous system
Prokinetics can be herbal, nutritional or pharmaceutical. Importantly, they are not laxatives. The aim is not urgency or frequency, but rhythm, coordination and timing.
What are prokinetics used for?
Prokinetics are commonly used in people with:
Recurrent or relapsing SIBO
IBS with bloating, constipation or mixed bowel habits
Functional Dyspepsia with early fullness, nausea or reflux
Symptoms that are worse overnight or between meals [3]
From a Brain-Body-Biome perspective, slowed gut motility is rarely random. It’s often influenced by:
Nervous system dysregulation (fight-or-flight dominance)
Inflammation
Previous infections or antibiotic use
Hormonal changes
Chronic under-eating or long-term restriction [4]
Prokinetics don’t fix these root causes on their own, but they can help create the conditions where other strategies finally start to work.
My experience with prokinetics
For me, prokinetics were a genuine turning point. I hadn’t realised how much of my pain was being driven by visceral hypersensitivity and gas pressure building between meals, rather than just reactions to food. My bloating was often worst when my stomach was empty (a real red flag for MMC dysfunction), and the pain could feel sharp, squeezing and constant. I initially used Prucalopride, but quickly realised I didn't need a prescription prokinetic and found several herbal alternatives which were equally effective for me.
Once motility was properly supported, that background pain began to settle, my bloating reduced significantly, and my pain lessened. Crucially, this happened while I was in the process of expanding my diet, not restricting it further. It really highlighted to me how central gut movement and nervous system signalling are in these conditions.
What are the best herbal prokinetics for SIBO, IBS and Functional Dyspepsia?
There is no single 'best' prokinetic for SIBO, IBS or Functional Dyspepsia. Different formulations suit different patterns, and tolerance matters. These are some commonly used options, with some context on when they might help.
None of these are ads - I’ve tried every one of these at some point during my own gut healing journey. That said, the prokinetic that worked best for me may not be the one that works best for you. Responses to prokinetics are highly individual, so if one doesn’t suit you, it’s often worth trying a different formulation rather than assuming prokinetics don’t work for you at all. This is also where working with a practitioner can be helpful, as timing, dose and nervous system context make a real difference.
Motility Activator - Integrative Therapeutics
The simplest formulation, containing just ginger extract and artichoke leaf. Ginger supports gastric emptying and coordinated contractions, while artichoke supports bile flow and upper GI motility. Often useful where bloating and fullness are dominant. Generally well tolerated - I would probably try this one first.
Bio.Revive Kinetic - Invivo
A broader blend including ginger, globe artichoke, citrus bioflavonoids, 5-HTP and B vitamins. May suit those with motility issues alongside fatigue, stress load or digestive insufficiency. This works best for me (it may not for you!).
Acetyl CH-Active - Apex Energetics
Supports acetylcholine, a key neurotransmitter involved in gut movement. Could be considered where motility issues overlap with nervous system depletion or poor gut-brain signalling.
MegaGuard - Microbiome Labs
Contains ginger, zinc carnosine, L-glutamine and mucosal-supportive nutrients. May be helpful when motility issues coexist with gastritis/peptic ulceration, gut lining irritation or sensitivity.
MotilPro - Pure Encapsulations
Includes 5-HTP, ginger, acetyl-L-carnitine and B vitamins. This is the 'trendy' prokinetic you read about online, but I actually liked it the least.
Iberogast
A liquid herbal preparation containing multiple bitters and carminatives. Commonly used in Functional Dyspepsia, particularly for nausea, reflux and early satiety. A gentle formulation that's generally well tolerated - best for upper GI symptoms (indigestion, heartburn, acid reflux, gastroparesis).
GI Motility Complex - Enzyme Science
Combines ginger, artichoke and apple cider vinegar. May suit those with suspected low stomach acid and who experience sluggish upper GI movement.
Lion’s Mane - Real Mushrooms
Not a traditional prokinetic, but relevant. Lion’s Mane may support nerve repair and gut–brain signalling, which can indirectly improve motility over time.
What pharmaceutical prokinetics exist?
There are also prescription prokinetics, which can only be used under the supervision of a doctor. These are sometimes considered when symptoms are more severe or persistent, or where there is clear evidence of impaired motility that hasn’t responded to other approaches.
Common examples include:
Prucalopride - Prucalopride is a serotonin (5-HT4) agonist that stimulates gut motility. It’s typically prescribed at a higher dose for chronic constipation, while lower doses are sometimes used specifically to support migrating motor complex (MMC) function. How it’s used depends very much on the individual clinical context.
Low-dose erythromycin - At low doses, erythromycin can act as a motility agent, particularly in the upper gut. However, it is still an antibiotic, and even at lower doses it may have antibiotic effects that can negatively impact the microbiome. This is an important consideration for people with SIBO or dysbiosis.
Domperidone and Metoclopramide - These medications are primarily used for chronic nausea, vomiting or gastroparesis, rather than for small-intestinal clearance or direct MMC support. Their role is more focused on gastric emptying and symptom control.
In some cases, pharmaceutical and herbal prokinetics may be used alongside each other under the supervision of a practitioner - for example, a prescription prokinetic before bed to support the MMC, with a herbal option used earlier in the day.
One important exception is 5-HTP. Prokinetics containing 5-HTP should be avoided when pharmaceutical prokinetics or SSRIs are being used, as combining agents that affect serotonin signalling isn’t appropriate without careful medical oversight due to the risk of serotonin syndrome.
As with everything in gut healing, these tools work best when used in context, alongside nervous system regulation, adequate nourishment, and an understanding of why motility slowed down in the first place.
When and how should prokinetics be taken?
For MMC support, timing is crucial.
Prokinetics are typically taken:
Before bed
At least 3-4 hours after your last meal
This matters because the MMC only switches on when the gut is in a true fasting state. Taking a prokinetic too close to food can interrupt this process, blunt its effect, or in some cases actually worsen symptoms by stimulating movement while digestion is still underway.
This was very clear in my own experience - when I took a prokinetic too near to food, my pain and visceral hypersensitivity noticeably worsened, rather than improved. Once I altered the timing of my dose, the same support became far more helpful.
Individual context is really important. We all have different gastric emptying and transit times, shaped by stress, hormones, inflammation and nourishment. For some people, a longer gap after eating is needed before the MMC can function properly, while others may tolerate a shorter window. This is one of the reasons prokinetics can feel unhelpful when the timing doesn’t quite line up - not because they’re the wrong tool.
Frequently asked questions about prokinetics
Do prokinetics help prevent SIBO relapse?
Yes - they are actually a key part of both treatment and relapse prevention, particularly when SIBO is driven by impaired gut motility. Research and clinical work has shown that supporting the migrating motor complex is central to clearing bacteria from the small intestine, and that prokinetics can play an active role not just after treatment, but as part of the treatment approach itself [5].
By improving small-intestinal clearance between meals, prokinetics help reduce the conditions that allow bacteria to accumulate and ferment again. This is why many people relapse quickly when motility isn’t addressed, even if antimicrobial or dietary strategies initially reduce symptoms [6].
That said, prokinetics work best within a broader Brain-Body-Biome framework. If the nervous system remains in a chronic fight-or-flight state, if inflammation is ongoing, or if someone is under-eating or heavily restricted, motility support alone may not be enough to prevent recurrence long term. In clinic, we often find that relapse prevention is strongest when motility, nervous system regulation, nourishment and individual root causes are addressed together.
Can prokinetics make symptoms worse at first?
Very occasionally. When gut movement increases, it can temporarily amplify sensations in a sensitive or inflamed gut, particularly where visceral hypersensitivity is present. This can show up as increased awareness of movement, bloating, discomfort, or pain - even though nothing harmful is happening. If this is the case, symptoms should ease within a few days of commencing the prokinetic.
Symptoms that continue to worsen after a few days can also be a sign that timing, formulation, or context isn’t quite right - for example, taking a prokinetic too close to food, using one that’s too stimulating, or supporting motility before calming the nervous system and inflammation. This is why individualisation matters, and why some people do better adjusting the approach rather than abandoning prokinetics altogether.
Are prokinetics safe to take long-term?
This depends on the type of prokinetic used and the individual context, which is why long-term use should always be reviewed thoughtfully rather than assumed to be right or wrong.
From a research perspective, there is evidence suggesting that in cases of post-infectious IBS and SIBO, impaired motility can be long-lasting rather than temporary. In these situations, ongoing prokinetic support may be appropriate for several years, and in some cases up to five years or more, to reduce the risk of relapse and support continued small-intestinal clearance.
That said, long-term use doesn’t mean forever. Tolerance, nervous system state, nutritional intake, microbiome health and symptom response all matter. Some people do well with sustained support, others need adjustments over time, and some may eventually taper once motility and gut-brain signalling are more resilient.
This is where context is everything. The goal isn’t to be on a prokinetic forever by default, but to use the right level of support for the right length of time, based on what’s actually driving symptoms.
Do I need a prokinetic if I don’t have constipation?
Yes, potentially, as prokinetics are not the same as laxatives. Their role is to modulate gut motility - meaning they help improve coordination, timing and flow through the digestive tract, rather than simply speeding everything up.
The migrating motor complex works independently of bowel frequency, so it’s entirely possible to have daily, regular stools and still have poor small-intestinal clearance. This is something we see frequently in SIBO and Functional Dyspepsia, where symptoms like bloating, pain, reflux or nausea occur between meals, not just around bowel movements.
Interestingly, prokinetics often appear to have a normalising effect. In a sluggish gut they can support movement, while in a gut that’s rushing or spasming they may actually help improve coordination and reduce chaotic contractions. This is one reason some people notice improvements in pain and bloating even without a change in stool frequency.
So the question isn’t really whether you’re constipated. It’s whether gut movement is well-timed, well-coordinated, and happening when it should, particularly between meals and overnight.
To sum up:
Prokinetics can be a powerful support for people with SIBO, IBS and Functional Dyspepsia, particularly where gut dysmotility and a sluggish migrating motor complex are part of the picture.
They are not a magic fix. But when used thoughtfully, at the right time, and alongside nervous system regulation, nourishment and root-cause work, they can be a crucial missing piece.
This is something we explore in depth in clinic, because formulation, timing and context make a real difference.
References:
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