Does melatonin help with digestive changes during perimenopause?

Digestive changes during perimenopause are more common than many women expect. Slower gut motility, increased gas, constipation, acid reflux, or more frequent loose stools can all emerge or worsen during this transition. The mechanisms involve declining progesterone (which slows gut movement), fluctuating estrogen (which affects gut bacteria and intestinal permeability), and heightened cortisol from disrupted sleep and stress. Melatonin has a more direct relationship with the gut than most people realize, though the evidence for supplementation specifically targeting perimenopause-related digestive changes is still limited.

Melatonin is best known as a sleep hormone produced by the pineal gland, but the gut is actually one of the largest reservoirs of melatonin in the body. Enterochromaffin cells in the gastrointestinal lining produce melatonin independently of the pineal gland, and melatonin receptors are found throughout the gut wall. This suggests melatonin plays a meaningful role in regulating gut function, not just sleep.

Research suggests melatonin helps coordinate gut motility through its interaction with the enteric nervous system. Circadian rhythms govern when the gut is most active and when it slows down for rest, and when your circadian rhythm is disrupted, as commonly happens during perimenopause due to declining melatonin and estrogen levels, digestive timing can become erratic. Taking supplemental melatonin may help restore a more regular circadian pattern, which in turn supports more predictable gut function.

Some small clinical trials have explored melatonin for irritable bowel syndrome (IBS) symptoms. A study by Lu et al. (2005) found that melatonin reduced abdominal pain and improved IBS symptoms in patients, though the study was small and not specific to perimenopausal women. The mechanism proposed involved melatonin's effects on gut motility and visceral pain perception. While this provides some plausibility for digestive benefits, it should not be overstated; the evidence is preliminary.

Melatonin's antioxidant and anti-inflammatory properties, reviewed by Rossignol and Frye (2011), may also protect the intestinal lining from oxidative damage. Gut permeability, sometimes called leaky gut, can increase during perimenopause, potentially worsening digestive symptoms. Melatonin's ability to reduce inflammatory signaling may offer some protective benefit here, though clinical data in perimenopausal women specifically is lacking.

Sleep quality is another indirect pathway. Toffol et al. (2014) documented lower melatonin levels in perimenopausal women alongside sleep complaints. Poor sleep raises cortisol, which disrupts gut motility and the gut microbiome composition. By improving sleep, melatonin may secondarily reduce the stress-driven digestive disturbances that compound hormonal changes.

Research has examined doses ranging from 0.3 mg to 3 mg. Zhdanova et al. (2001) found that 0.3 mg was effective for sleep improvement in middle-aged women with fewer side effects than higher doses. Studies on gut-specific outcomes in IBS populations have used doses up to 3 mg. Talk to your healthcare provider about the right dose for your situation, particularly if you have a diagnosed gastrointestinal condition.

Safety: melatonin is generally well tolerated for short-term use. Higher doses may cause next-day drowsiness. It can interact with blood thinners, immunosuppressants, and some diabetes medications. People with autoimmune conditions should consult their provider before use.

For digestive changes during perimenopause, melatonin is unlikely to be the primary solution but may complement other strategies. Dietary adjustments, probiotic support, regular physical activity, and stress management all have stronger evidence for gut health. If you are tracking your cycle phases and symptoms in PeriPlan, noting when digestive symptoms flare relative to your cycle can help you and your provider identify whether hormone fluctuations or other factors are the main driver.

When to see a doctor: New or changing digestive symptoms always deserve medical attention, especially if they include blood in the stool, unexplained weight loss, severe abdominal pain, or persistent changes in bowel habits. These can signal conditions such as colorectal cancer, inflammatory bowel disease, or celiac disease that require proper diagnosis and are not related to perimenopause. Do not assume digestive changes are hormonal without a proper evaluation.

This content is for informational purposes only and does not replace medical advice. Always consult your healthcare provider about your specific situation.