Train Your Gut to Stop Runner’s Trots & Cramps

You can train your gut to minimize runner’s trots and tummy troubles during the marathon. They key is to practice fueling on your long runs, aiming to take in an energy gel every half hour, and fluids about every mile. Learn how.

Being a runner has many wonderful side effects but one of them is NOT runner’s trots or runner’s stomach—diarrhea that endurance runners experience when going the distance. In fact, GI distress and running almost go hand in hand. I mean, it’s no coincidence that “runs” is a double entendre. “My long runs give me long runs…” You get the picture.

Whitney Heins running a marathon
Gut training is key for success in the marathon!

But new science in runner’s nutrition has unlocked a new fueling strategy for runners to stop runners stomach, runners trots, runners cramps, runners diarrhea, and bonking: gut training.

In fact, gut training could be just what you need to accomplish that next big PR. 

My first experience with bonking & runner’s trots

gut training for runners
Pin these gut training tips for later.

I ran my first marathon in college—the Marine Corps Marathon, in honor of my former Marine dad who ran this race every year when I was a kid. As a student at Georgetown University, the start was right down the street from my apartment, and I trained using a Jeff Galloway plan that I tailored to my own needs.

Related: 6 Best Energy Gels for Runners

I honestly didn’t really know what I was doing. I didn’t pay attention to mobility or rest days. And I certainly didn’t pay attention to fueling for running—unless you count plenty of beer the night before I ran. 

I felt great during the marathon until I hit the wall (aka bonking) when my stomach started cramping…bad. I was able to jog-walk to the finish and get my goal time of a Boston-Qualifying 3:29. Then it was straight to the bathroom. Repeatedly.

I remember meeting my parents and boyfriend for a celebratory meal afterward, only to spend the whole time in the bathroom.

Related: The Scientific Benefits of Long Runs

What are runners trots?

Runners trot, runners stomach, or runners diarrhea is an intense urge to poop during or right after you run. Some of the symptoms of runners trots or runners stomach include bloating, stomach cramps, diarrhea, nausea, vomiting, chest pain, heartburn, and the extreme urge to poop. 

What causes runners trots or runners stomach?

The causes for runners trot, runners stomach, or runners diarrhea vary. It could be that you’re nervous, eating and drinking the wrong foods before your run, using the wrong fuel during your run, or not drinking enough (dehydration). If you feel intense pain during your run, stop running. 

Related: Hydration Tips for Runners

Gut training can stop GI distress in runners & unlock your next PR

Stomach cramps while running, diarrhea while running, and GI distress for runners are no laughing matter.

I have known many athletes who trained hard for goal races only to have all that hard work undone by tummy troubles while running or bonk (which is when you experience glycogen depletion). In fact, in my last two marathons, I didn’t fuel the last 10 miles or so of the race because my stomach just couldn’t handle the gels.

Laura Norris, head coach for The Mother Runners, says to start small building from 30 to 60 grams of carbs per hour.
Laura Norris, head coach for The Mother Runners, says to start small building from 30 to 60 grams of carbs per hour.

But fueling during long-distance races is crucial, as your body burns through its glycogen stores within 2 hours (or less) of running. The trouble is just when your body needs fuel the most to keep going, it can’t digest said fuel because it doesn’t have the blood flow to do so (all the blood is diverted to your extremities).

Related: How to Pick the Best Energy Gel for Running

To avoid bonking, you need to teach your body how to breakdown the fuel with what it has available to it, explains Laura Norris, co-coach at The Mother Runners.

Research shows that the optimal amount of carbohydrate intake for performance in the marathon distance (and beyond) is 50-60g of carbohydrates per hour – which is a lot!” shares Laura who has written about how runners can train their guts. “For most people, if you just started out on this, you would have GI distress. However, your gut (like any muscle) can be trained.”

Learning how to train your gut could be the difference between achieving your PR or running for the bushes.

Training Your Gut for Athletic Performance

You can avoid runners stomach, runners trots, and runners diarrhea, and GET THOSE PR’s by training your gut much as you train your legs and lungs to go the distance. To get the details on gut training, I went to Dana Eshelman, MS, RDN, owner/CEO of A Dash of Dana Nutrition Coaching, a nutritionist who specifies in working with endurance athletes.

How to Stop Runner’s Stomach, Runner’s Cramps, & Runner’s Trots

To prime you for all the gut training knowledge Eshelman shares, here are 10 key takeaways for training your gut to avoid runner GI distress:

  1. Train your gut to learn how to digest carbs and drinks during training at least 2-3 weeks before your event.
  2. Aim to consume roughly 60 grams of carbs per hour of your training and/or race.
  3. Switch up your carb source so that some have fructose and some have glucose. But do not mix sports drinks with gels in a single serving.
  4. Avoid foods high in fiber, fat, and protein before and during running.
  5. Monitor your diet by keeping a food journal 2-3 days before your long runs to learn what could be causing GI distress.
  6. Eat foods high in simple carbs before endurance running events and races like white rice, white potatoes, white pasta, and bananas.
  7. Avoid medicating to eliminate GI distress during runs.
  8. Stay hydrated before, during, and after your long run or race.
  9. Eat on a regular schedule, particularly before big runs or races.
  10. Practice your race-day nutrition on your long runs.

What is gut training?

Gut training
Dana Eshelman, an endurance athlete and a nutritionist, says gut training could be the difference between bonking and a PR.

The term “training your gut” describes a way to reduce the GI stress that often occurs during endurance running or race day. If you are an endurance athlete, chances are you have experienced this exercise-induced GI stress such as cramping, nausea, runners diarrhea, and/or vomiting.

“If you have had a poor experience (or many missed attempts) at fueling during exercise, you are not the odd one out. This is common. As the research shows, the body is adaptable and by practicing a fueling and hydration plan, you can improve your carbohydrate tolerance over time,” says Dana. 

Why do you get diarrhea after a long run or other tummy troubles?

Digestion normally occurs at rest when there is adequate blood flow to the gut allowing for the absorption of nutrients and secretion of digestive enzymes, explains Dana.

Exercise causes stress on the body and a shift in blood flow away from the gut causing changes in GI motility, absorption of nutrients, and secretion of enzymes that aid in digestion. This causes malabsorption and causes a poor appetite, leading the athlete to not intake much-needed hydration or fuel (like me during my last couple of marathons).

Unfortunately, under-fueling and dehydration can cause additional GI distress and GI distress may be exacerbated by the intake of fuel and fluids during exercise. This leaves the endurance runner between a rock and a hard place. But don’t lose hope!

“In order for an athlete to tolerate more hydration and fuel to support performance and prevent GI dysfunction, they must train their gut!” says Dana.

What does “train your gut” mean?

Training your gut essentially means you get used to taking in hydration and fuel before and during your workouts. You train it to get used to working (digesting) when it has less blood flow.

Why should a runner train their gut?

Lots of research shows that consuming carbs during exercise helps maintain intensity and delay the onset time of exhaustion, especially at higher intensity. New research shows the gut is highly adaptable and can accommodate changes in fueling through gene expression induced by sugar consumption. How cool is that? And, it doesn’t take a long time to do this.

The evidence indicates there is a two-to-three-week period of increasing carbohydrate intake during exercise to allow for adequate fueling and improved GI tolerance.

But, just as you wouldn’t run in new shoes for the first time on race day, it’s important you do a dress rehearsal for your fueling technique before race day. “Your hydration plan is also of significant importance as this can help control GI distress and dehydration may exacerbate stress on the gut,” Dana reminds us.

Related: 3 Proven Ways to Re-fuel After a Long Run

How to Train Your Gut & Stop Runner’s Stomach
Learning how to train your gut for long-distance training will keep you from taking frequent potty stops.

How to train your gut for marathon fueling or endurance running

The Academy of Nutrition and Dietetics recommends 30-60 grams of carbohydrate per hour of exercise and up to 90 grams of carbohydrate for endurance events lasting longer than three hours, shares Dana.

If you are someone that trains fasted, or not eating anything pre-workout, starting off consuming 30-60 grams of carbohydrate before or during a workout may seem overwhelming and will likely cause GI distress. Therefore, it’s important to start small, says Dana and Laura:

  • Begin with what you can tolerate (likely 30 grams per hour)
  • Gradually, increase the amount and frequency of your fueling on your long runs, e.g. a gel every 45 minutes, then increase frequency every 5 minutes.
  • Aim for a gel every 30 minutes on race day.

Pay attention to how you feel as depending on the duration of your workout, you may need more or less carbs.

  • Research suggests for running 1-2 hours, aim for 30 grams an hour.
  • For running 2-3 hours, aim for 60 grams per hour. For running more than 3 hours, aim for 90 grams of carbs per hour along with 20 grams of protein in 5-7 increments.
  • Changing up your carb source has also been shown to improve performance as it triggers different receptors in the body, allowing for improved oxidation rates.

Gut training fueling technique examples:

  Start Here Making Progress Goal Nutrition + Hydration

1-4 g/kg carbs in the 1-4 hours before exercise

1⁄2 piece of fruit + 1 T nut butter + 12- 16 ounces water


1⁄2 slice toast + 1 jam + 1 T nut butter + 12- 16 ounces water

12-15 grams carbs

1 piece of fruit + 1 T nut butter + 12- 16 ounces water


1 slice toast + 1 T honey + 1 T nut butter + 12- 16 ounces water

25- 30 grams carbs

1 piece of fruit + 1 T nut butter + 1 T honey + 1 slice toast + 12- 16 ounces water

50-60 grams carbs

During workout

30-60 g carb/ hour of exercise lasting longer than 1 hour

1-2 sports gummies OR

1⁄2 scoop drink mix in 32 ounces water

7-10 grams carbs

3 sports gummies OR

1 scoop drink mix in 32 ounces water

20- 25 grams carbs

6 sports gummies OR
2 scoops drink mix in 32 ounces water
3 sports gummies + 1 scoop drink mix in 32 ounces water45-60 grams carbs

In the pre-workout phase, you want to focus on adequate carbohydrates and low to moderate fiber, fat, and protein foods. Carbohydrates are important for adequately fueling your muscles and topping off your energy stores, especially in workouts lasting longer than an hour. Fiber, fat, and protein will slow down digestion, which we want to avoid pre-workout.

What to eat for marathon fueling

These components should be consumed in meals and snacks throughout the day.

Pre-workout examples to work toward with 1- 4 hours before:

  • 1 banana + 1 T nut butter (25 grams carb)
  • 1⁄2 c oats + 1⁄4 c dried fruit (55 grams carb)
  • 1 pita pocket + 2 T hummus (26 grams carb)
  • Small sweet potato + 1/4 c Greek yogurt (20 grams carb)
  • Bob’s oat bar (28 grams carb)
  • 1 c honey bunches of oats + almond milk (47 grams carb)
  • Dave’s Bread + 1 banana + 1 tsp honey (54 grams carb)

Pre-workout examples to work toward with 15-45 minutes before:

  • 1⁄4 c dried fruit (20 grams carb)
  • 6 oz real fruit juice or sports drink (20-25 grams carb)
  • 1 c fruit smoothie (20-25 grams carb)
  • Honey packet (15 grams carb)

During your workouts longer than 1-hour examples to work toward:

**remember staying hydrated decreases GI distress

  • 1 scoop drink mix + 32 ounces water such as Skratch, Maurten, Nuun Endurance or Tailwind (20-25 grams carb)
  • 2 scoop drink mix + 32 ounces water (40-50 grams carb)
  • 6 energy chews such as Honey Stinger, ProBar Bolt, or Skratch (~45 grams carb)
  • 1 energy gel such as Untapped, Honey Stinger, Maurten, or GU (20-25 grams carb)
Gut training
Teaching your stomach to intake fuel with decreased blood flow can dramatically improve your performance.

How to implement gut training

Dana advises starting gut training by evaluating your current hydration and fueling plan. Pick one area to target and build from there. Try a small snack pre-workout, determine if that is enough or too much, adjust the timing of fueling and hydration, and continue to tweak based on energy, tolerance, and workout goals.

For workouts longer than one hour, add in hydration and fuel from the “Start Here” column above and decide if this is appropriate for your performance goals. Your fueling and hydration plan should be individual to you, and it often takes time to figure out your secret potion.

“Keep in mind, just like training, not all days are treated equally; your fuel and hydration needs will vary from day-to-day. Adequate training of the gut with both carbohydrate and hydration leads to a less dramatic decrease of blood flow with increased exercise intensities, which is important in preventing GI symptoms,” explains Dana.

If after taking these steps, you are chronically experiencing GI distress with increasing training duration and intensity, you may consider consulting a sports dietitian to find your optimal fueling and hydration technique.

If you want guidance with your running goals, check out my run coaching services. Also, be sure to check out my free training plans:

5 thoughts on “Train Your Gut to Stop Runner’s Trots & Cramps”

  1. I’m glad I found this article. I’d hardly describe myself as an endurance athlete but this has been plaguing me since last year. Seemingly out of nowhere I have developed a serious problem. Once incident – after only 8km cross country – led to a week in hospital. There are no culprits according to all of the testing: no infection; excellent cardiac results; colonoscopy all clear; no IBD or Crohn’s; no allergies or intolerances; etc, etc. Incredibly frustrating. Currently training for a 20k trail run and its happening again after 5k. Will be giving this a try! PS does T=teaspoon? 🙂

    • I hope it helps Kathleen! It may be helpful to keep track of when it acts up. If it is outside running, doing a GI map may be helpful as it could be a symptom of a gut imbalance…

    • Capital T means tablespoon
      Lowercase t means teaspoon

      Hope you feel better Kathleen. I struggle with this also and the article was super helpful to me too!


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