Can You Train Your Gut to Tolerate Gels During Long Runs?

Many runners struggle to digest carbohydrates before or during runs. This can lead to unpleasant symptoms like urgency to use the bathroom, gut discomfort, or pain during and after exercise.

These issues are commonly referred to as “runner’s gut.”

What is Runner’s Gut?

Runner’s gut includes symptoms such as:

• Urge to go to the toilet mid-run

• Diarrhea

• Cramping or side stitches

• Bloating or gas

• Nausea or reflux

Why Does Runner’s Gut Happen?

1. Reduced blood flow to the gut

During exercise, blood is redirected to working muscles. This can reduce blood flow to the gut by up to 80%, leading to:

• Poor digestion

• Gut irritation

• Increased gut permeability (“leaky gut”)

2. Mechanical impact

Running creates a repetitive “jostling” effect on the intestines, which can:

• Speed up bowel movements

• Trigger urgency

• Contribute to diarrhea

3. Nutrition-related triggers

Common dietary causes include:

• Too much fibre before running

• High-fat foods

• Large meals too close to exercise

• Highly concentrated carbohydrate products

• Dehydration

• Trying new or unfamiliar foods/products

4. Carbohydrate malabsorption

If you consume more carbohydrate than your gut can absorb:

• Carbohydrates remain in the intestine

• Water is drawn in → diarrhea

• Bacteria ferment carbs → gas and bloating

• Less carbohydrate is delivered to muscles

This is a key area that can be improved through gut training.

5. Dehydration

Dehydration can:

• Reduce digestion efficiency

• Increase stress on the gut lining

• Worsen GI symptoms

6. Stress and the nervous system

The gut and brain are closely connected. Stress and race-day nerves can:

• Increase gut motility

• Worsen urgency and discomfort

What Is Your Gut?

Your “gut” refers to your gastrointestinal tract (stomach and intestines).

The walls of the gut contain smooth muscle, which helps move food through the system via rhythmic contractions.

Unlike skeletal muscles (like your quads or biceps), this muscle is not under conscious control. However, the speed and efficiency of digestion can still change based on factors like exercise, stress, and nutrition.

Can Your Gut Adapt?

While smooth muscle itself doesn’t “grow” like skeletal muscle, your gut can adapt functionally.

Adaptations include:

• Increased enzyme activity

• Improved carbohydrate transporter capacity

• Better tolerance to food and fluids during exercise

This is the foundation of gut training.

How to Train Your Gut to Tolerate Carbs

Step 1: Optimise your pre-run nutrition

• Practice your pre-run meal regularly

• Aim for:

  • 20-40g carbs 15-30 minutes before (eg.2 medjool dates), or

  • 1 g/kg carbs 45–60 minutes before (eg. 2 slices toast and honey), or

  • 2 g/kg carbs 2–3 hours before (eg. Big bowl jasmine rice and powerade). 

• Keep meals low in fibre and fat

• Avoid large volumes if eating close to your run

Step 2: Start low and build up

Begin with:

• 30–40 g carbohydrates per hour (1 gel)

Gradually increase every 2–3 weeks toward:

• 60–90 g/hour (most runners)

• Up to 100–120 g/hour (advanced/elite)

Step 3: Train during long runs

Your long runs should act as race-day rehearsals.

• Practice fueling during these sessions

• Include some efforts at race pace

• Higher intensity increases gut stress, making practice essential

Step 4: Use multiple transportable carbohydrates

Look for products containing:

• Glucose + fructose (≈2:1 ratio)

Why this matters:

• Different transporters absorb each type

• Increases total carbohydrate absorption

• Reduces risk of gut overload

Step 5: Be consistent

• Minimum effective period: ~2 weeks

• Practice fueling multiple times per week

Consistency is key to adaptation.

Step 6: Match race conditions

Train exactly how you plan to race:

• Same gels or drinks

• Same timing (e.g. every 20–30 minutes)

• Similar intensity

Step 7: Adjust if needed

If symptoms persist:

• Trial different products

• Consider hydrogels or isotonic options, which may be easier to tolerate

• Check your overall fueling strategy (timing, dose, concentration)

• Check if this gel requires water during ingestion. 

Key Takeaways

• The gut is adaptable and trainable

• Don’t give up after one or two bad experiences

• Practice fueling regularly to improve tolerance

Simple framework:

• Start at 30–40 g carbs/hour

• Build to 60–90 g+

• Practice 1–2 times per week

• Use glucose + fructose

• Train at race pace

For more support with training your gut, book a 1:1 consult here.