Most people think of serotonin as a chemical in the brain.

But the reality is that your gut actually produces more than 90% of your body's serotonin. This is where it does the essential work of controlling your digestion and creating a direct link between your gut health and mental wellbeing.

I'm Manny, founder of Fifth Ray. After battling Crohn's Disease for 16 years, I transformed my health through understanding how the gut works, and I've seen firsthand how gut function impacts overall wellbeing.

In this article, you'll discover why your gut is the primary place serotonin is created in your body, how your gut bacteria control serotonin levels, and what this means for your digestion and mental health.

Your Gut Makes Serotonin to Control Digestion

Your gut produces over 90% of your body's serotonin in specialised cells that line your intestines. These cells, called enterochromaffin (EC) cells, are spread throughout your digestive tract, constantly monitoring what's happening in your gut.

When these EC cells detect food, stretching in your intestines, or chemical signals, they release serotonin to coordinate these processes. This triggers responses that control how food moves through your system, adjust digestive fluids, manage nausea, and regulate pain signals.

This is why your gut produces so much serotonin. It's not there to regulate your mood. It's there to manage the constant work of digestion.

Does Gut Bacteria Control Serotonin Production?

Yes, your gut bacteria directly control how much serotonin your EC cells produce. They do this by managing tryptophan, the building block your body uses to make serotonin.

Certain bacteria stimulate your EC cells to produce more serotonin by creating compounds called short-chain fatty acids.

Research shows that removing gut bacteria causes serotonin levels to drop significantly, and they return to normal when bacteria is restored. This proves how essential your gut bacteria are for serotonin production.

This creates a feedback loop. Serotonin affects which bacteria thrive in your gut, while those bacteria control how much serotonin gets made.

This is why taking care of your gut bacteria is essential for maintaining healthy serotonin levels and proper digestion.

How Does Gut Serotonin Affect Your Mood?

The serotonin in your gut stays in your gut. It can't cross into your bloodstream to reach your brain, so it doesn't directly affect your mood.

However, gut serotonin activates the vagus nerve. This nerve carries messages about what's happening in your gut to the parts of your brain that control mood and emotions.

This means changes in gut serotonin can indirectly influence how you feel. When serotonin levels or signalling get disrupted in your gut, that information travels to your brain through the vagus nerve.

But the connection works both ways.

Your brain can also influence gut serotonin release, which is why stress affects your digestion. Your mental state impacts your gut, and your gut impacts your mental state.

What Happens When Your Gut Serotonin Levels Are Low?

Low gut serotonin slows down digestion, causing constipation, bloating, and that uncomfortable feeling that you never quite empty your bowels completely.

Without enough serotonin, the muscles that push food through your digestive system don't contract as they should.

Low serotonin also makes your gut overly sensitive. Normal digestion starts to feel uncomfortable or even painful.

Because gut serotonin sends signals to your brain through the vagus nerve, low levels are linked to anxiety, low mood, and poor sleep. When something goes wrong in your gut, that message travels up to your brain and affects your emotional state.

Is There a Link Between Gut Serotonin and IBS?

Yes, IBS is strongly linked to disrupted serotonin signalling in the gut. Research shows that people with IBS have abnormal serotonin levels and signalling patterns compared to healthy individuals.

How this shows up depends on which type of IBS you have.

In IBS-D, the form characterised by diarrhoea, excess serotonin activity speeds up gut transit, causing food to move through the digestive system too quickly.

In IBS-C, the constipation-predominant form, reduced serotonin availability slows transit, leaving people feeling blocked and uncomfortable.

Many IBS medications work by targeting gut serotonin receptors to control digestion speed and reduce pain. These treatments demonstrate how central serotonin function is to digestive health and symptom management.

How to Support Healthy Gut Serotonin Production

Here’s what you can do to support healthy serotonin production in your gut.

Eat fibre-rich foods to feed the beneficial bacteria that help your gut produce serotonin. When you eat dietary fibre, you're feeding the gut microbes that create compounds which signal your intestinal cells to make more serotonin.

Include fermented foods like sauerkraut, kimchi, kefir, and yoghurt to build a diverse gut microbiome. These foods introduce helpful bacteria that support the conversion of tryptophan into serotonin.

Manage stress, because chronic stress disrupts both your gut bacteria and serotonin signalling. When you're under stress, hormones change the composition of your gut bacteria and interfere with normal serotonin release, which affects both your digestion and your mood.

Cosmic Hue combines seven plants that support the gut environment where serotonin is produced. These include marshmallow root that coats the gut lining where serotonin-producing cells work, and ashwagandha that reduces stress that disrupts gut-brain communication.

Conclusion

Your gut produces over 90% of your body's serotonin to manage the essential processes of digestion, from moving food through your system to controlling how your gut responds to discomfort.

Your gut bacteria directly control how much serotonin gets made, and while this serotonin stays in your digestive tract, it communicates with your brain through the vagus nerve, connecting your gut health to your mental wellbeing.

Supporting gut health through diet, stress management, and gut-supportive plants like those in Cosmic Hue helps maintain healthy serotonin production.

Author: Manny is the founder of Fifth Ray and a certified Gut Health Coach. After battling Crohn's Disease for 16 years, he transformed his gut health through plant-based healing. His story has been featured on BBC, ITV, and Daily Mail.

Disclaimer: This information is for education only. Cosmic Hue is not intended to diagnose, treat, cure, or prevent any disease. Always speak to your healthcare provider before changing your routine.

References

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