How to Train Your Gut to Tolerate Gels for Long Runs
Your gut can be trained, just like your legs.
Have you ever tried a gel on a run, felt nauseous or bloated, and decided that “gels just don’t agree with me”?
You’re not alone. GI symptoms are common in runners, particularly during longer or harder sessions. The good news is that your gut can adapt to taking in carbohydrate and fluid during exercise. With regular practice, you can improve your tolerance and build towards the fuelling strategy you’ll need to perform your best on race day.
Why Take Gels During Long Runs?
Gels, chews and sports drinks are convenient ways to consume carbohydrates while running.
Carbohydrate provides an important fuel source for working muscles, particularly as exercise intensity increases. Taking carbohydrate during longer runs can help maintain blood glucose and carbohydrate availability, reduce the perception of effort and fatigue, and support endurance performance.
For longer training sessions and races, fuelling isn't just about finishing the run , it's about being able to maintain your pace and recover well afterwards.
Why Carbohydrate — Not Fat or Protein?
Your body uses both carbohydrate and fat for energy during exercise, but carbohydrate becomes increasingly important as intensity increases.
Carbohydrate can be rapidly digested and absorbed, allowing glucose to become available to working muscles. This is why most sports gels are primarily carbohydrate-based.
Fat and protein are slower to digest and can delay stomach emptying. Consuming large amounts of either immediately before or during a run may increase the likelihood of fullness, nausea or other GI symptoms.
Why Do Gels Cause Gut Upset?
What runners call “runner’s gut” can have several causes. It isn't necessarily the gel itself.
1. Reduced blood flow to the gut
During exercise, blood flow is prioritised towards working muscles and other tissues involved in thermoregulation. This can reduce gastrointestinal blood flow and affect digestion, particularly during harder or longer efforts.
2. Mechanical movement
The repetitive impact of running can irritate the gastrointestinal tract and increase gut motility. This can contribute to cramping, urgency or diarrhoea in some runners.
3. What you eat before running
Common triggers include:
Large meals too close to running
High-fat foods
High-fibre foods
Excessive caffeine
Trying unfamiliar foods or supplements
Starting a run dehydrated
4. Too much carbohydrate too soon
If you suddenly increase your carbohydrate intake during a run, your gut may not be accustomed to handling it.
When carbohydrate isn't absorbed efficiently, it can remain in the intestine and draw water into the gut, potentially contributing to bloating, cramping or diarrhoea.
This is particularly relevant when consuming higher carbohydrate intakes. Combining multiple carbohydrate transportable sugars, such as glucose/maltodextrin and fructose, can increase the amount of carbohydrate that can be absorbed compared with relying on glucose alone.
5. Dehydration
Starting a run dehydrated or becoming significantly dehydrated during exercise can worsen GI symptoms and make carbohydrate intake harder to tolerate.
6. Stress and nerves
Your brain and gut are closely connected. Feeling anxious, rushed or nervous before or during a race can increase gut motility and contribute to urgency, nausea or discomfort.
So, Can You Actually Train Your Gut?
Yes.
Your gastrointestinal system can adapt to regular carbohydrate intake during exercise. This research paper by Asker E Jeukendrup in 2017, suggests repeated practice can improve carbohydrate absorption and tranport capacity, gastric emptying and overall tolerance to consuming food and fluid while exercising.
Your gut doesn't “grow” like your muscles do, but it can become better at handling and absorbing carbohydrate during exercise.
How to Train Your Gut
1. Start small
If you're new to gels, don't jump straight into a high-carbohydrate fuelling strategy.
Start around 30–40 g carbohydrate per hour and gradually increase based on your tolerance and training goals.
For example, start with one gel per hour, or even practise taking half a gel at a time.
2. Practise regularly
Aim to practise your fuelling strategy 1–2 times per week rather than only on your longest run.
Your gut needs repeated exposure to carbohydrate during exercise.
3. Build gradually
Every 1–2 weeks, gradually increase the amount of carbohydrate you're consuming if your gut is tolerating it well.
A longer-term goal for many endurance runners is 60–90 g+ carbohydrate per hour, depending on the duration and intensity of the event and individual tolerance.
You don't need to reach this immediately.
4. Use multiple carbohydrate sources
When consuming higher carbohydrate intakes, products containing a combination of glucose/maltodextrin and fructose can help maximise carbohydrate absorption.
Many sports products use this approach, including products from brands such as Maurten, Precision Fuel & Hydration and SiS.
5. Practise at race intensity
Start practising your fuelling on easier long runs where your gut is under less stress.
As tolerance improves, practise taking gels during tempo, intervals and race-pace sessions.
The goal is for race day fuelling to feel familiar — not experimental.
6. Don't forget hydration
Carbohydrate and fluid intake need to work together. Make sure you're starting your run adequately hydrated and practise your hydration strategy alongside your gels.
7. Consider the bigger picture
Your gel may not be the only reason you're experiencing gut symptoms.
Look at your 24 hours before the run as well as your immediate pre-run meal. Consider whether you're consuming unusually high amounts of fibre, fat, caffeine or food volume before running.
A Simple Gut-Training Framework
Weeks 1–2:
30–40 g carbohydrate/hour
Weeks 3–4:
40–60 g carbohydrate/hour
Following weeks:
Gradually build towards 60–90 g+ carbohydrate/hour, if appropriate for your event and tolerance.
Practise 1–2 times per week, starting during easier runs before progressing to race pace.
Remember: these are general guidelines. Your ideal carbohydrate target depends on your body size, exercise duration, intensity and individual tolerance.
Key Takeaways
Your gut is adaptable and can be trained.
One bad experience with a gel doesn't mean you can't tolerate carbohydrate while running.
Start with a manageable amount and gradually increase your intake.
Practise your fuelling regularly — not just on race day.
Consider the type, amount and timing of carbohydrate, as well as hydration and your pre-run nutrition.
If you're aiming for higher carbohydrate intakes, glucose/maltodextrin + fructose products can be useful.
Don't wait until race day to test your strategy!
Need help training your gut?
If you're struggling wit1. Jeukendrup AE. Training the Gut for Athletes. Sports Medicine. 2017.h gels, bloating, nausea, diarrhoea or figuring out how much carbohydrate you actually need, individualised support can help.
Book a 1:1 consultation to develop a personalised fuelling strategy and troubleshoot your gut symptoms while training.
References:
Jeukendrup AE. Training the Gut for Athletes. Sports Medicine. 2017. https://pubmed.ncbi.nlm.nih.gov/28332114/
Costa RJS et al. The Effect of Gut Training and Feeding. Sports Medicine. 2023. https://pubmed.ncbi.nlm.nih.gov/37061651/
