Home/Journal/Melatonin and Gut Health: Can a Healthy Gut Help You Sleep Better?
Gut, Skin, Hair And Internal WellnessJul 31, 2026 · 7 min read

Melatonin and Gut Health: Can a Healthy Gut Help You Sleep Better?

Your gut does more than digesting your food. Learn how it may influence your melatonin, sleep quality, and overall well-being.

M
By Maryam
Clinical Nutritionist
A woman calmly sleeping in a white bed, illustrating the connection between melatonin and gut health and how healthy habits may support better sleep naturally.

This is one of the suffering that my clients routinely describe when they’re struggling with poor sleep and digestive discomfort. I've been going under a lot of pressure . It’s been such a hectic days that I am just falling into bed every day.

I have been lying awake for hours trying to fall asleep but unable to. The next day I wake up feeling terrible – another boring day ahead of me because I lack energy. This is because I ate at night at 10 PM instead of during lunch time. Of course it does! Because when I sleep less, I feel lethargic.

Also, whenever I eat late or too frequently, my digestion gets affected badly. What does this even mean for me though? They struggled with their both physical and mental health without knowing the reason. They lead me to find the connection between melatonin and gut health.

But then I read a few studies over the past year showing a connection between our bodies’ production of melatonin, which controls our sleep cycles, and the state of our gut microbiome — trillions of microorganisms living inside us that help regulate everything from digestion to immunity to mood and beyond — and everything changed.

Turns out we’re far more connected than we ever thought possible. For example, we know about the role that melatonin plays in regulating our sleep, but fewer people realize that this hormone is also produced in our GI tract. Yes, we are aware of the gut microbiome which includes both beneficial and harmful bacteria, and maybe even that these microorganisms interact with the body.

Woman holding her stomach with digestive discomfort, illustrating how gut health may be connected to sleep and the role of melatonin and gut health in overall wellness.
You've been focusing on your sleep... but what if your gut is the real conversation starter?

What Is Melatonin?

Most people know about the role of melatonin – sometimes referred to as “the sleep hormone”. But, I will explain shortly for who don’t have any idea. This important chemical substance is largely manufactured by the pineal gland in your brain, where production increases in the dark time. High concentrations of melatonin signals to your body it’s time to get ready for bed as we go through our natural daily cycle (our circadian rhythm), as in night.

Healthy melatonin production supports:

  • Falling asleep at the early night time
  • Maintaining your healthy sleep-wake cycle
  • Adjusting to your changes in light and darkness
  • Supporting overall circadian rhythm regulation
  • Also, melatonin is made by the gastrointestinal tract.
  • There, researchers think that melatonin has roles involving things like digestion and protecting your gut, but don’t believe that it makes you sleepy.
Woman sleeping peacefully in a dark bedroom, illustrating healthy melatonin production, restful sleep, and nighttime wellness.
Melatonin is your body's natural sleep hormone—not just a supplement. Learn how healthy habits can support its natural rhythm for more restful nights.

Does Your Gut Produce Melatonin?

But one of the most surprising discoveries we’ve made in recent years was that our bodies produce substantial quantities of melatonin in the digestive tract itself. Even though this doesn’t exactly put us “to sleep,” there’s evidence that these melatonin production sites play some role in supporting healthy digestion. How melatonin and gut health provides benefit to you:

Protect the Gut Lining

Your digestive tract is lined with tissue that serves as a protective barrier between what’s going on inside your body and various substances moving through your intestines. When it functions properly, your barrier prevents harmful substances such as bacteria, microbial toxins, and undigested food particles from entering to your bloodstream.

The condition known as “leaky gut” bacteria where in result it become weakened or permeable, and partially digested food start pass through your intestinal lining, triggering immune reaction in you and cause inflammation. Melatonin helps in this in supporting gut barrier by promoting repair of intestinal cells and reduce damages cause by inflammation. 1

Simple illustration showing how melatonin and gut health are connected, with melatonin supporting a stronger gut barrier and healthy intestinal lining.
Melatonin does more than support sleep—it may also help maintain a healthy gut barrier, highlighting the fascinating connection between melatonin and gut health.

Reduces Gut Inflammation

Melatonin has anti-inflammatory properties that may help people who suffer from digestive disorders such as inflammatory bowel disease and inflammatory bowel syndrome and it may also helpful in the healing of intestinal ulcers.

May Reduce Acid Reflux Symptoms

Gastroesophageal reflux disease (GERD), a condition where your stomach acid flows back into esophagus, causing heartburn and stomach irritation in you. Melatonin may help patients in GERD by supporting function of your lower esophageal sphincter, it is your muscle that prevents your stomach contents from moving back into the esophagus. When melatonin added with Proton Pump Inhibitors (PPI) mainly with omeprazole, symptoms improve more better. 2

The Gut Microbiome and Sleep: A Two-Way Conversation

When many different types of beneficial microbes are present in the gut microbiome (a healthy balance), they help support our digestion and even communicate with the brain using chemical messengers. Sometimes this balance is disrupted — sometimes referred to as gut dysbiosis — which can cause changes to these communications too.

It reduces to reduced serotonin and melatonin production in gut. If there aren’t enough probiotic gut bacteria to break down your tryptophan and create serotonin, your brain will not not have enough supplies to produce melatonin to get you good night’s sleep. Interesting point is 95% of serotonin is produced in the gut. 3

While they both were seem like entirely separate activities in your body to you, but now you know how melatonin and gut health share an incredible number of connections that you wouldn’t even think about at first.

Connection between mental health, sleep quality, gut health, and melatonin production showing how the gut brain axis influences the sleep cycle
Melatonin helps regulate sleep, but its story starts with the gut-brain connection. Supporting gut health, managing stress, and practicing healthy sleep habits can help your natural sleep rhythm.

Foods That Naturally Contain or Support Melatonin

No food is able to increase melatonin levels dramatically; however, some foods contain very small amounts of this hormone that regulates your sleep. Others contain nutrients that stimulate your natural production of melatonin.

  1. 1.Tart Cherries are one of the most popular natural sources of melatonin and have been studied for their impact on better night's sleep. 4
  2. 2.Pistachios, in addition to being high in melatonin content, are rich in fat and fiber as well.
  3. 3.Walnuts are high in omega 3-fatty acid; they also have a small quantity of melatonin.
  4. 4.Oats are rich in complex carbohydrates as well as other natural tryptophan and melatonin and hence assist in eating nutritious dinner.
  5. 5.Kiwi consumption before going to bed can also provide you the improved quality of sleep for some individuals. Further studies will be needed to prove this assumption.
  6. 6.Milk and Dairy Foods contains such substances that improve your sleep as it has melatonin and tryptophan that is necessary for the production of serotonin and melatonin.
  7. 7.Eggs has been discovered contain high quality protein as well as nutrients (e.g.,
    things like tryptophan to make melatonin naturally.
  8. 8.Salmon, sardines and mackerel have a lot of vitamin D and melatonin. Help you sleep well.
  9. 9.Bananas are full of things like carbohydrates, potassium, magnesium, tryptophan and vitamin B6. These are good, for relaxing your muscle and help your body make melatonin.
  10. 10.Eat more fiber every day. It is great food for the gut bacteria. These foods will make your gut happy. Here are some sources of fiber you can eat:

Lentils, Beans, Apples, Berries, Broccoli, Carrots, Chia seeds, Flax seeds, Whole grains

You should always drink more water when eating fiber to keep your stomach happy and avoid any upset. If you’re eating healthy and fiber foods, and it makes you still bloated, then I also write a detailed guide for this problem that how to get rid of it easily without excluding anything from your diet!

Melatonin-rich foods chart featuring natural foods that support healthy sleep and the body's natural sleep-wake cycle.
Some foods naturally contain melatonin, while others provide nutrients that support your body's normal melatonin production and a healthy sleep–wake cycle. Pair these foods with good sleep habits for the best results.

Lifestyle Habits That Support Melatonin And Gut Health

The quality of your sleep is not just about what goes on once you get into bed. Daily practices have an impact on both melatonin levels and your gut. Some of those include:

  • Getting into a routine for sleeping, The human body is designed to thrive on routine. Waking up and sleeping at similar hours on both weekdays and weekends will help you maintain your circadian rhythm.
  • Being exposed to natural light during the daytime.
  • Reducing screen exposure at night.
  • Exercising regularly.
  • Learning how to reduce stress through relaxing practices.
  • Having a regular diet.
  • Not smoking and drinking responsibly.
  • Drinking enough water.
  • Expose to day sunlight: Natural daylight soon after waking helps regulate your circadian rhythm, which supports your healthy melatonin production later in the evening. 5
  • Create a Screen-Free Wind-Down Routine: Using phones, tablets, and computers that produce bright light at night may interfere with the secretion of melatonin in your body. Think about reducing lighting and screen time before sleeping.
    None of these tips take immediate effect, but all of them build an atmosphere that allows healthy digestion and healthy sleep cycles.

The human body is designed to thrive on routine. Waking up and sleeping at similar hours on both weekdays and weekends will help you maintain your circadian rhythm.

Clean bedroom prepared for sleep with a sleep mask, glass of water, and cozy bed, representing healthy bedtime habits for melatonin and gut health.
A calm bedtime routine can support your body's natural melatonin rhythm and complement healthy gut habits. Small evening rituals can make a big difference for restful sleep.

Be Patient With Your Body

Bacteria in the gut take time to change, just as sleep patterns do. Good practices carried out over weeks and months will be more helpful than a quick fix.

Melatonin Supplements

You can take Melatonin supplements when you have trouble sleeping because of any thing like jet lag or a new work schedule. Sometimes Melatonin helps people fall asleep.. I do not think Melatonin is good for all sleep problems. Melatonin is for some sleep issues. 6

You can use Melatonin supplements for a time to help you sleep better. Melatonin can be helpful for people who have trouble sleeping because of a change, in their schedule. It does not improve gut health as well. It is always important to consult a doctor prior to taking Melatonin.

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further reading —

References

  1. 1.Lindsay Curtis (2026, March 21) Melatonin Isn't Just for Sleep—It's Essential for Your Gut Too, verywell health view source ↗
  2. 2.Malekpour, H., Noori, A., Abdi, S., Abbasinazari, M., Mahboubi, A., & Ghamsari, M. A. (2023). Is the Addition of Sublingual Melatonin to Omeprazole Superior to Omeprazole Alone in the Management of Gastroesophageal Reflux Disease Symptoms: A Clinical Trial. Turkish Journal of Gastroenterology, 34(12), 1206–1211. https://doi.org/10.5152/tjg.2023.23021 view source ↗
  3. 3.Your Gut Microbiome’s Surprising Role in Melatonin Production, (2025, July 11) Just Thrive view source ↗
  4. 4.Howatson G, Bell PG, Tallent J, Middleton B, McHugh MP, Ellis J. Effect of tart cherry juice (Prunus cerasus) on melatonin levels and enhanced sleep quality. Eur J Nutr. 2012 Dec;51(8):909-16. doi: 10.1007/s00394-011-0263-7. Epub 2011 Oct 30. PMID: 22038497. view source ↗
  5. 5.de Menezes-Júnior LAA, Sabião TDS, Carraro JCC, Machado-Coelho GLL, Meireles AL. The role of sunlight in sleep regulation: analysis of morning, evening and late exposure. BMC Public Health. 2025 Oct 6;25(1):3362. doi: 10.1186/s12889-025-24618-8. PMID: 41053799; PMCID: PMC12502225. view source ↗
  6. 6.Who can and cannot take melatonin (2026, February 23), NHS https://www.nhs.uk/medicines/melatonin/who-can-and-cannot-take-melatonin/ view source ↗
quick answers —

Frequently asked questions

Melatonin supplements may be helpful for some people in the short term, but they are not appropriate for everyone. It's best to speak with your healthcare professional before taking melatonin regularly, especially if you are pregnant, breastfeeding, have a medical condition, or take other medications.
Yes. Poor or irregular sleep may alter your balance of gut bacteria, potentially affecting your digestion, metabolism, and overall gut health. This relationship works both ways.
Some studies suggest melatonin may help support your protective lining of the esophagus and stomach, but it should not replace standard treatments for GERD. But the combination of your Proton Pump Inhibitors with the melatonin show more improvement in symptoms. Speak with your healthcare provider before using melatonin for acid reflux.
Melatonin supplements are primarily used to help regulate your sleep in certain situations. They should not be taken specifically for gut health without medical advice, as more evidence is needed regarding their benefits for digestive conditions.
Early research suggests melatonin may help support the intestinal barrier and maintain the health of your gut lining. However, more human studies are needed, and melatonin should not be considered a treatment for increased intestinal permeability ("leaky gut") without medical guidance.
For most healthy adults, melatonin is generally considered safe for short-term use when taken as directed. However, melatonin is primarily used to help regulate the sleep–wake cycle and is not an approved treatment for gut inflammation. Although early research suggests it may support your intestinal barrier and normal inflammatory responses, more high-quality human studies are needed. If you have a chronic digestive condition, are pregnant or breastfeeding, or take prescription medications, consult your healthcare provider before using melatonin supplements.
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