Running with IBS: How Exercise Can Actually Improve Symptoms

How I wish I could outrun my IBS… but is that even possible?

With 25,000 runners gearing up for Perth’s City to Surf and 35,000 for the Sydney Marathon this weekend, running season is officially in full swing. If you’re managing IBS and lacing up those running shoes, you’re not alone. Frustratingly, running can both improve and worsen gut symptoms, depending on how you do it. Since making my 2020 New Year’s resolution to start running consistently, I’ve learned first-hand what helps and what doesn’t. Here are my top 6 strategies for running with IBS, backed by the latest science and a dash of gut-friendly banter.

What science says about IBS and exercise

Research in the past few years confirms that:

• Moderate-intensity exercise (like jogging or run/walk intervals) can reduce IBS symptom severity and improve quality of life. Read more here 👉🏽

• High-intensity or long-duration running (e.g. marathons) may increase gut permeability and worsen diarrhea or cramping. Read more here 👉🏽

• Exercise influences the gut-brain axis - helping regulate stress, which is a known IBS trigger. Read more here 👉🏽

• Running boosts microbial diversity over time, enhancing the diversity of beneficial gut bacteria such as Lactobacillus and Bifidobacterium which produces anti-inflammatory short-chain fatty acids and supports gut barrier integrity. Read more here 👉🏽

👉 Translation: Running is good for your gut but… high intensity speed workouts and long distance endurance runs can increase the risk of GI distress and therefore needs to be managed carefully.

Practical tips for running with IBS

1. Watch your fuel

Skip sports gels, isotonic drinks, fruit juices and energy chews. Most are packed with high fodmap sugars like fructose and/or polyols.

If your require mid-run fuel, test options such as stuffed dates, along with certified low fodmap protein bars and lollies. And make sure you’ve thoroughly gut-tested your race day fuel during training.

💡 Smart fuel tip: Superflora Gut Health Shakes are certified low fodmap, gentle on the stomach, and contain prebiotic fibre + probiotics. With 25g+ of protein, they make a great post-run recovery shake without triggering symptoms.

2. Stay hydrated

Dehydration is a recipe for cramps and gut flare-ups. Water is always best. If you need electrolytes, choose low fodmap-certified options, if you can find them. I get it! There’s so much hype about ‘natural electrolytes’ in coconut water. Coconut water is tempting but the recommended low fodmap serving size is only 100ml which isn’t going to get you far unless you dilute it with water. I tend to alternate between water, home-made gels and frozen Hydralytes. Most Hydralyte drinks are made with glucose and electrolytes without high fodmap sweeteners. Avoid anything with fructose, honey and agave as sweeteners, and any “hydrating” drinks with ingredients that end in '‘-ol’ like sorbitol, mannitol or xylitol. And test, test, test during training runs.

3. Time your meals

The blanket rule regarding food timing is to avoid eating 60-90 minutes before a run to prevent bloating, hiccups or reflux. But does this advice work for runners with IBS? Typically, fermentable carbohydrates take 2-3 hours to reach the lower intestine where they ferment and cause trouble. But studies show that gut motility can increase by up to 30% during moderate to vigorous exercise, meaning foods may move faster into the large intestine, potentially triggering gas, bloating, or urgent bowel movements sooner than expected. And just to complicate things further, running shunts blood away from your gut and into your muscles, slowing digestion - while at the same time speeding up gut motility lower down. This mismatch helps explain why reflux, bloating, or urgent toilet stops can appear suddenly and without warning during a run - regardless of how careful you are. What fun! That’s why smaller, lighter meals or snacks (such as bananas) are better tolerated before a run. But have I mentioned that you’ll need to test, test, test during training runs??!! Nothing new on race day. Ever.

4. Plan for emergencies

Even with the best preparation, IBS can still catch you off guard mid-run. That’s why planning for emergencies is key. Research shows that up to 30–50% of runners experience some form of “runner’s gut” - from cramping to urgent bathroom stops - and the risk is even higher in people with IBS. A smart strategy is to map out your route in advance using Google Maps so you know where public toilets are located. And for peace of mind, keep a small “disaster kit” handy: a change of clothes, wet wipes and toilet paper in the car, and even a pack of tissues in your running backpack. Most of the time, you won’t need it - but just knowing it’s there can reduce anxiety and make running feel more manageable.

5. Manage caffeine & triggers

Caffeine is a double-edged sword: yes, it can improve performance but also trigger urgent bowel movements. Test your tolerance on training days, well ahead of race day. If you have a long run planned, try taking a caffeine gel in the second half of your race – this might allow you to benefit from the caffeine but give you enough time to get to the finish line without a bathroom break. The impact of caffeine is so individual but us IBS-peeps tend to have good intuition about our own tolerance level so listen to your gut!

6. Don’t forget iron & energy

If you’re following a long-term low FODMAP diet, it’s worth keeping an eye on your iron intake during training. Iron plays a crucial role in transporting oxygen to your muscles via haemoglobin, and low levels are strongly linked to fatigue and reduced endurance. In fact, studies show that up to 20–25% of female athletes experience iron deficiency, which can significantly impair running performance and recovery. Endurance training itself also increases your iron needs, as foot-strike impact and gut irritation from running can contribute to small but chronic iron losses. Alongside iron-rich foods, don’t neglect your energy stores: gut-friendly carbs such as red rice, gluten-free pasta, or sourdough spelt are excellent options for pre-race carb loading. Balancing iron and carbohydrate intake can make the difference between running out of steam mid-race and finishing strong.

Adjusting for IBS flare-ups

IBS flare-ups can derail even the best training plan, but listening to your body is as important as clocking the kilometres. On bad days, consider run/walk intervals - research shows that alternating running and walking reduces gastrointestinal stress by lowering intra-abdominal pressure and giving your gut more time to settle. If symptoms persist, switch to gentle movement such as yoga, Pilates, or walking; studies highlight that low-intensity exercise can help regulate gut motility and reduce perceived stress, both common IBS triggers.

And remember, rest is not failure - it’s a key part of training. Recovery days allow your gut, muscles and nervous system to reset, and overtraining during a flare can prolong symptoms and increase your risk of injury. By adapting instead of pushing through, you’re more likely to bounce back stronger for your next session.

Even with the occasional flare-up, running brings surprising benefits:

• Stress release (key for IBS management)

• Improved gut microbiome over time

• Community & routine (hello, ParkRun!)

For me, my weekly 5km ParkRun has become a non-negotiable - through heatwaves, rainy days, exams, family dramas and flare-ups, it’s always worth it. Running with mates is simply the best!

Takeaway: IBS-friendly running is possible

The key is to listen to your gut, fuel smartly, and stay consistent. Running won’t cure IBS, but it can help manage symptoms, improve resilience, and bring joy back into movement.

💡 Want gut-friendly fuel to support your running? Try our Superflora Gut Health Shakes - packed with prebiotic fibre, probiotics and protein for gentle energy and recovery.

Written by: Noisy Guts CEO Dr Josephine Muir, an enthusiastic but very recreational runner who is positively miserable at the prospect of missing the Sydney Marathon this year but hopes to sign up for a new goal event soon.