How to Train Your Runners Gut

Do you always have stomach pain after running? Here are 5 tips you can start today to train your runners gut and GI system.

male and female talking and running on a trail

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Runners gut, or experiencing unpleasant symptoms before, during or after running, is a common phenomenon in the running community.

In fact, it is estimated that between 30 and 90% of runners experience some form of gastrointestinal disturbance.

Yikes! That’s a wide range, but it’s also likely that you have experienced some form of runners belly or an upset stomach while running.

While it is probable that this has to do with nutritional issues, which this post will discuss, it can also be attributed to dehydration, certain medications, high levels of stress and anxiety, or maybe even genetics.

Why Should We Care About Fixing Abdominal Pain When Running?

Well, obviously running with an upset stomach is not comfortable. But secondly, it impacts your performance. So figuring out what should you eat before a run is important!

If you’re having to stop every so often to go to the bathroom or stifling that need and pushing through, your pace is most likely suffering.

Rather than focusing on your running goals, you’re stuck on wondering where the closest bathroom is or how to hold it just a little bit longer.

Some of the common symptoms experienced during “running digestion” include:

  • Belching
  • Reflux/heartburn
  • Abdominal pain or cramping
  • Nausea or vomiting
  • Diarrhea
  • Bloating
  • Urge to defecate

Why Do You Experience GI Issues After a Long Run?

You’re probably here because at some point or another, you’ve googled or wondered, “Why does my stomach hurt after running?”

Of interest, runners are more likely than other athletes to experience these adverse symptoms, and understanding when should you carb load.

A lot of people joke that running and bowel issues go hand in hand. It doesn’t have to be that way.

Part of it may not be eating the right types of carbohydrates

Here are some good carbs for runners that may help mitigate any runners stomach symptoms.

woman tired after a run

Some reasons your stomach may hurt when running long distances are:

  • The up-and-down jostling that occurs while running
  • The speed at which you’re running
  • Reduction of splanchnic blood flow during exercise – When exercising, blood is going to the limbs rather than to the gut, so anything in the stomach just “sits” there and can be uncomfortable
  • Decreased gastric motility and emptying
  • Hormone shifts
  • Neuroendocrine-Gastrointestinal pathway – An increase in sympathetic activation, which reduces GI function
  • Hotter weather can exacerbate symptoms
  • Eating high fat and protein-rich foods before a run (eggs for muscle building should be eaten post-workout)

Save those protein shakes for running for after your workout.

In addition to slowing you down and impacting your performance, all of this discomfort and running with an upset stomach can also result in nutrient malabsorption, which can further exacerbate symptoms and performance.

Not getting the necessary carbohydrates and electrolytes needed for long-distance exercise can lead to underperformance but can also be dangerous in some situations.

Nutrient malabsorption can also lead to more water content left in the small intestine, which can lead to increased gas production or runners gut bacteria, thanks to bacterial fermentation (or our gut microbiome).

How Long Does Runners Stomach Last?

The symptoms of runners stomach, or any repercussions, such as runner’s diarrhea, may last up to 12-24 hours.  However, much of this will be individual.

Proper nutrition, hydration and recovery can reduce the time one experiences these adverse symptoms.

If you continue to experience runner’s trots, or runner’s diarrhea longer than 24 hours after a run, it may be a signal of another underlying medical condition, such as irritable bowel syndrome (IBS).

Definitely consult with your doctor for other avenues of treatment in such circumstances.

black running shoes on a street before a run

Nutritional Recommendations For Runners Gut

While the ultimate goal is to prevent cramps with running, it may not be entirely possible because we are fluid humans, and some days, certain foods may affect us more than others.

However, these nutritional changes and recommendations should generally help decrease the feelings of a stomach ache when running or an upset stomach after running.

1. Limit Fiber Before a Long Run

Some people may want to limit sources of fiber, like complex carbohydrates (grains, legumes, certain fruits and vegetables) before a run.

Those who are extra sensitive may want to limit these foods a day or two before a long run, though this usually requires trialing.

Sometimes, a modified LOW FODMAP diet can also help symptoms, though it’s not something someone should be following without guidance from a dietitian due to the restrictive nature and loss of key nutrients that would need to be replaced elsewhere.

loaf of white bread

We have an episode that digs deep into the Low FODMAP diet for runners.

High fiber foods are likely to cause more discomfort since they take longer to digest and in other words, sit in the stomach for longer.

This may be pertinent to a vegan ultra runner who eats many fruits and vegetables and grains. 

Anyone practicing trail running nutrition should be aware of the variety in the diet.

Instead, try quick-acting, easily digestible carbs before a run, like:

  • Glass of juice
  • White bread with peanut butter or jelly
  • Half a banana
  • Scoop of UCan powder
Ucan fueling
Click here to order

Try some of these breakfasts for runners, too!

You may also want to check out our post on the best marathon fuel for a sensitive stomach.  

2. Don’t Go Into a Run Dehydrated 

Our hydration needs are dependent on many things, such as our body size, the weather, the altitude, and how trained a person is for exercise. The average person sweats 1-2 liters per hour.

Sweating reduces the blood volume and ingesting adequate water and electrolytes helps restore the blood volume to normal levels.

Before Exercise: Consume eight ounces of fluid 15-30 minutes prior and 16 ounces a few hours before.

During Exercise: Keep a good handheld bottle with you to help you accomplish 0.4-0.8 L/hour. To be more precise, this will depend on your sweat rate. The goal is to prevent excessive dehydration, which is a greater than 2% loss of body weight.

After Exercise: Drink 16-24 ounces for each pound lost during exercise to help replenish lost fluids and electrolytes.

group of women running on trails

We talk more about hydration and specific conditions in the Nail Your Nutrition Course and in this guide for hydration for running

Don’t forget the value of hydrating foods as well, such as many fruits and vegetables.

3. Limit or Avoid Caffeine Before a Run

While caffeine can be a stimulant and ergogenic aid and caffeine before running may be beneficial for some, it won’t work for everyone.

For those with sensitive stomachs, it can cause increased anxiety, which can lead to a slew of uncomfortable gut symptoms.

Research studies conclude that 3-6mg/kg body weight of caffeine ingested 60 minutes before a workout can be helpful for performance. However, for someone with a sensitive stomach or caffeine sensitivity, perhaps start with a much smaller amount.

Or even consider decaf coffee, or a tea instead.

Be careful of certain gels and fueling products with caffeine and even pre-workout which can have a slew of different substances.

Here is more information about coffee vs. pre-workout

3 mugs of coffee; coffee beans, ground coffee and brewed coffee

4. Beware of Certain Ingredients, like Artificial Sweeteners

Typically, anything ended in -ol” can also be problematic for some people because although they aren’t “sugar,” they refer to sugar alcohols.

Sugar alcohols can just ferment and cause discomfort in the gut. Therefore, ingredients, like maltitol, sorbitol and xylitol should be limited or avoided before exercise.

Products like diet soft drinks, no-sugar sweetened dairy products, Quest bars, Think Thin, One Bars, Lenny & Larry’s cookies and no-sugar products should be avoided.

If you regularly consume these, you may want to think about taking them out of your half marathon diet.

5. Add Probiotics

Probiotics refer to the live bacteria throughout our bodies but mostly concentrated in our intestines and digestive system. Probiotics may lower the incidence of GI symptoms, decrease inflammation, and even help with recovery.

There’s a lot of research to come on probiotics and how different strains may be beneficial for athletes vs. non-athletes.

For example, a 2011 randomized control trial in cyclists found that probiotics reduced GI symptoms and symptoms of upper respiratory tract illness.

A good brand Probiotics is Thorne Research.

Are probiotics going to cure everything? They likely won’t solve all of your abdominal pain when running, but they can certainly help your gut in general.

How to Train Your Gut

You may have heard that you can train your gut, but what does that really mean?

Well, with practice, your GI system can adapt to taking in fuel during your run, which will also minimize the risk of hitting the wall in a marathon. But to do so, you have to be eating carbohydrates regularly, meaning not following a low carb diet or keto diet for runners

There are several different carbohydrate-based fueling options out there to experiment with.

Ucan orange energy tub

Let’s tie everything together when considering the proper nutritional recommendations for training your gut for running.

Some things to consider when training your gut include:

  • How much fuel to take in
  • When to take your calories
  • How much water to take alongside your carbohydrates
  • The speed or pace at which you are exercising

These fuels and running gels for sensitive stomachs may be a better option for those who experience running and stomach problems.

You also may want to experiment with different forms of sports nutrition. Some people prefer and handle gels well; others prefer running chews

Huma plus gel

UCAN – The superstarch in UCAN is more easily digested and keeps blood sugar and energy more stable during longer endurance exercise. Mix it with water 30 minutes to an hour before your run, or add it to your water bottle during your run.

If you’re a salty sweater, make sure you’re accounting for that sodium!

Ucan fueling
Click here to order

Tailwind – Tailwind is an all-in-one fueling option, meaning it provides hydration, electrolytes and carbohydrates in one. For those who are sensitive to solids during exercise, this is a great option because it’s all liquid. Just mix into your water bottle!

Huma Gels – Huma gels are lighter on the stomach, made with chia seeds.

Muir – Muir gels are made with “real food,” like blackstrap molasses, sea salt, passionfruit, pineapple and more. They have slow and quick acting gels.

Want your running nutrition questions answered?
Fill out this form to be matched with one of our sports dietitians.


  • Costa RJS, Snipe RMJ, Kitic CM, Gibson PR. Systematic review: exercise-induced gastrointestinal syndrome—implications for health and intestinal disease. Aliment Pharmacol Ther. 2017.
  • Karhu E, Forsgård RA, Alanko L, Alfthan H, Pussinen P, Hämäläinen E, et al. Exercise and gastrointestinal symptoms: running-induced changes in intestinal permeability and markers of gastrointestinal function in asymptomatic and symptomatic runners. Eur J Appl Physiol 2017;
  • Mora-Rodríguez R, Pallarés JG, López-Gullón JM, López- Samanes Á, Fernández-Elías VE, Ortega JF. Improvements on neuromuscular performance with caffeine ingestion depend on the time-of-day. J Sci Med Sport. 2015;18(3):338–42.
  • Parnell JA, Wagner-Jones K, Madden RF, Erdman KA. Dietary restrictions in endurance runners to mitigate exercise-induced gastrointestinal symptoms. J Int Soc Sports Nutr. 2020 Jun 10;17(1):32. doi: 10.1186/s12970-020-00361-w. PMID: 32522222; PMCID: PMC7288429.
  • West NP, Pyne DB, Cripps AW, Hopkins WG, Eskesen DC, Jairath A, Christophersen CT, Conlon MA, Fricker PA. Lactobacillus fermentum (PCC®) supplementation and gastrointestinal and respiratory-tract illness symptoms: a randomised control trial in athletes. Nutr J. 2011 Apr 11;10:30. doi: 10.1186/1475-2891-10-30. PMID: 21477383; PMCID: PMC3083335. 
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