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.
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.
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
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.
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.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.Pistachios, in addition to being high in melatonin content, are rich in fat and fiber as well.
- 3.Walnuts are high in omega 3-fatty acid; they also have a small quantity of melatonin.
- 4.Oats are rich in complex carbohydrates as well as other natural tryptophan and melatonin and hence assist in eating nutritious dinner.
- 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.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.Eggs has been discovered contain high quality protein as well as nutrients (e.g.,
things like tryptophan to make melatonin naturally. - 8.Salmon, sardines and mackerel have a lot of vitamin D and melatonin. Help you sleep well.
- 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.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!
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.
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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References
- 1.Lindsay Curtis (2026, March 21) Melatonin Isn't Just for Sleep—It's Essential for Your Gut Too, verywell health view source ↗
- 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.Your Gut Microbiome’s Surprising Role in Melatonin Production, (2025, July 11) Just Thrive view source ↗
- 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.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.Who can and cannot take melatonin (2026, February 23), NHS https://www.nhs.uk/medicines/melatonin/who-can-and-cannot-take-melatonin/ view source ↗
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