Can Over-Exercising Trigger an IBD Flare?

My Experience & How to Exercise Safely

For seven years, I kept my inflammatory bowel disease (IBD) in remission. I exercised consistently but mindfully, focusing on walking, yoga and Pilates, which worked beautifully for me. They kept me strong, flexible and calm.

But then, I decided to push harder as I thought I needed to do more weight training and gym work to get fitter in my post-menopause years. Many days, I was spending over an hour on the cross-trainer and weightlifting and crowing about my achievement. Some friends thought it a bit mad ☺

I told myself I was getting fitter, stronger and healthier. But deep down, I knew I was doing it to lose weight and to prove that I could push myself harder than ever. (Over achiever!)

At first, I felt good. I was pleased with my discipline and my progress. But my body wasn’t as impressed. The warning signs were there: abnormal tiredness, disrupted sleep, slight digestive changes. I ignored them. I thought it was just me getting old. It started subtly and I didn’t listen to my body. Before I knew it, I was dealing with a full-blown IBD flare, completely undoing the remission I’d maintained for seven years.

Looking back, I think I know what happened. Over-exercising had pushed my body into stress mode, raising inflammation, increasing gut permeability and weakening my gut lining. That was at least some of the cause of this flare. 

To be fair, I did not have any idea that over-exercising could potentially contribute to a flare. This experience forced me to reassess how to exercise safely with IBD, ensuring movement supports, rather than worsens, my health.

This is what I learnt:

Over-exercising can trigger an IBD flare

It’s easy to assume that the more exercise you do, the better. Howver, for those of us with IBD, that’s not true. Over-exercising can stress the body in ways that aren’t immediately obvious:

Increased gut permeability (leaky gut)

Long, intense exercise, especially endurance cardio, can increase intestinal permeability, meaning that toxins and bacteria that should stay in the digestive system start leaking into the bloodstream. This can cause an immune response and increase inflammation, making it a potential flare trigger for people with IBD.

Raised Cortisol (Stress Hormone)

Exercise is a stressor. In moderate amounts, it’s a good stressor, helping to regulate inflammation. But too much raises cortisol levels, which increase inflammation, weaken the lining of the gut and disrupt the body's ability to recover.

Reduced blood flow to the gut

During high-intensity exercise, the body redirects blood flow from the digestive system to the muscles. This means the gut recieves less oxygen and fewer nutrients, which may increase inflammation, cramping and digestive distress.

Nutrient depletion

People with IBD already have higher nutritional needs, especially for magnesium, zinc, iron, B vitamins and electrolytes. Over-exercising burns through these at an even faster rate, which can cause fatigue, slower healing and increased inflammation.

Reduces beneficial bacteria

Important gut bacteria such as bifidobactera and lactobacillus are reduced which creates an imbalance in the microbiome which may allow for an increase in pro-inflammatory bacteria.

Digestive symptoms from overtraining

Have you ever noticed that intense exercise can result in bloating, cramping or even diarrhoea? That’s because excessive movement, combined with the release of stress hormones, can cause gut spasms and irritation—things you don’t want if you have IBD.

How to exercise safely with IBD

After my flare, I made a major shift in how I approach exercise. Here’s what is advised:

Choosing the right type of exercise for IBD

Low-impact cardio: Walking, swimming, and cycling at a comfortable pace support fitness without excess strain.

Strength training: Weightlifting is still great, but I allow plenty of recovery time.

Breathing and relaxation: Incorporating mindful breathing and movement balances the nervous system and reduces inflammation. Yoga is a perfect blend with the right instructor (yoga approaches do vary; some are gentler than others).

Modify exercise based on your energy levels

Instead of forcing yourself to push through fatigue, listen to your body. The rule I follow is:
“Exercise should leave me feeling better, not more exhausted.”

Think about recovery and take one or two rest days per week instead of pushing through. On these days, focus on gentle movement like stretching, easy swimming or gentle yoga.

Instead of an hour-plus of cardio every day, I now limit it to 30 to 45 minutes. I balance higher-intensity and lower-intensity workouts to allow my body to recover.

Support hydration and nutrition

It is always a good idea to think about your fluid intake and especially if you have IBD or have had proctocolectomy, ileostomy or colostomy. You also need more water during a flare and after surgeries.

I focus on anti-inflammatory foods like omega-3-rich fish and colourful vegetables. I can tolerate a lot of fibrous foods but eat as many plants as your digestive system can cope with comfortably and eat enough protein, especially if weight training. You need the amino acids from protein foods to support the repair of the lining of the colon.

Finding balance when exercising with IBD

Now I am more aware of my flare signs, I take those as time to reduce my output, relax more and adjust my diet. I’m finding a balance between movement that keeps me strong and that which supports my body and wellbeing.

If you’re struggling with exercise and IBD, ask yourself:

Does your exercise routine leave you feeling energised or exhausted?

Are you listening to your body’s signals, or pushing through discomfort?

Are you prioritising recovery as much as effort?

Listen to your body. It is very wise!