Why Melatonin Supplements Aren’t Working: How Nutrition and Thyroid Health Affect Sleep

You’ve tried everything. The magnesium gummies, the melatonin spray, the sleepy time teas. You’ve turned your bedroom into a cave and put your phone on airplane mode by 9 p.m. Maybe you even stopped scrolling and started meditating, hoping that this would finally fix your sleep.

But your eyes still pop open at 2:17 a.m.

Or maybe your body feels tired, but your brain just. won’t. shut. off. You toss and turn, counting sheep, ceiling tiles, how many hours of sleep you’d get if you fell asleep right now.

If you’ve ever felt like your sleep is fragile, broken, or just plain hard to come by, especially when you’re doing all the “right things,” this post is for you.

We’re going to dig into what actually builds melatonin in your body (hint: it’s not just taking melatonin), the nutrients and food patterns that make or break your sleep quality, and how your thyroid ties into all of it. Because when thyroid hormones are low or poorly utilized, sleep often becomes a downstream casualty.

The Sleep Struggle Is Real, And You’re Not Alone

Most of the women we work with come to us with some version of this story:

“I eat pretty well. I’m not drinking a ton of caffeine. I try to unwind before bed. But I’m still exhausted. I wake up feeling like I haven’t slept at all.”

Or:

“I fall asleep okay, but I wake up in the middle of the night almost every night, and then I can’t fall back asleep.”

Or this one:

“I’ve been told my labs are normal. That my sleep issues are ‘just stress.’ But I feel like something deeper is going on.”

And they’re right. There is something deeper. And it starts with the chemistry of how your body makes melatonin.

How Your Body Actually Makes Melatonin

Melatonin is your body’s sleep hormone. It helps you feel sleepy, stay asleep, and keep your circadian rhythm in sync.

But melatonin isn’t just something your body turns on when the lights go out. It has to be built from nutrients, enzymes, amino acids, and a whole lot of metabolic teamwork. That process requires energy, and energy metabolism is regulated heavily by your thyroid hormones, particularly T3.

The process looks like this:

Tryptophan (amino acid) → 5-HTP → Serotonin → Melatonin

Each of these steps needs very specific ingredients and proper metabolic function. If you’re missing one, or if your thyroid isn’t firing well, the whole process can slow down.

Nutrients That Build Melatonin (And What Happens When You’re Deficient)

Let’s break down the key players:

• Tryptophan

Found in protein-rich foods (turkey, eggs, seeds), this amino acid is the raw material. But it competes with other amino acids to get into the brain. You need a small insulin spike (from carbohydrates) to help tryptophan win the race.

• Iron

Cofactor for tryptophan hydroxylase, the enzyme that converts tryptophan to 5-HTP. Low iron means the pathway bottlenecks at the very start. Common in women with heavy periods or Hashimoto’s.

• Vitamin B6 (P5P)

Crucial for converting 5-HTP to serotonin. It also helps convert serotonin to melatonin. Depleted by stress, alcohol, hormonal birth control, and poor liver function.

• Magnesium

Supports enzymatic activity in both serotonin and melatonin synthesis. Also helps calm the nervous system. Many people with hypothyroidism are deficient due to gut malabsorption or high stress.

• Folate & B12

Needed for methylation, which helps with neurotransmitter balance and the final step of melatonin synthesis. If methylation is sluggish (common with MTHFR or low stomach acid), your body may struggle to complete the conversion.

• Zinc

Helps stabilize enzymes and supports B6 activation. Zinc deficiency is frequently seen in hypothyroid individuals, especially when gut function is impaired.

• SAMe

S-adenosylmethionine is required to convert serotonin into melatonin. It’s produced via methylation pathways, which are supported by B12, folate, choline, and protein. Poor methylation or high oxidative stress can deplete SAMe and interrupt the process.

• Carbohydrates + Protein

Protein supplies tryptophan. Carbs help tryptophan cross the blood-brain barrier. Too little of either, and your serotonin-melatonin pipeline slows down.

What Does This Have to Do With Your Thyroid?

Your thyroid hormones regulate the pace and efficiency of every cell in your body, including the ones involved in neurotransmitter and hormone production.

Low T3 or poor conversion of T4 to T3 can:

• Lower your body temperature, which slows enzyme activity (enzymes are temperature-sensitive!)
• Reduce ATP production, making your cells less efficient at converting nutrients into neurotransmitters
• Impair gut motility and digestion, leading to nutrient malabsorption
• Disrupt cortisol patterns, which throws off melatonin timing

So even if you’re eating all the right foods, you may not be using them well if thyroid function is low or sluggish at the cellular level.

This is often why we see clients with “normal” labs, yet they’re still bloated, foggy, and exhausted—even after 8 hours in bed.

Why Low-Carb Diets Can Disrupt Sleep

This one surprises a lot of people.

When you don’t eat enough carbohydrates, especially in the evening, your insulin stays low. That might sound like a good thing—until you realize insulin helps tryptophan get into the brain.

Without that support, tryptophan struggles to compete with other amino acids and never makes it across the blood-brain barrier. Which means serotonin and melatonin don’t get made.

This is why we often see women on low-carb or keto diets struggle with insomnia, irritability, or the classic “tired but wired” pattern.

A balanced dinner with protein and a complex carb (like root veggies, fruit, or squash) helps the body shift into melatonin mode. And for thyroid health, adequate carb intake supports T3 production and helps prevent the body from downshifting into metabolic conservation mode.

What About Gut Health?

Your gut is deeply involved in this story. Here’s how:

• About 90% of your serotonin is made in the gut
• Your gut also produces melatonin (not just your brain!)
• Inflammation or dysbiosis can impair tryptophan metabolism
• Poor gut health = poor nutrient absorption = missing melatonin cofactors

Plus, a sluggish thyroid slows down digestion, stomach acid production, and gut motility—creating the perfect storm for dysbiosis, bloating, and bacterial overgrowth, which can further interfere with sleep quality.

Cortisol, Blood Sugar, and the Melatonin Tug-of-War

Your circadian rhythm is a coordinated dance between melatonin and cortisol.

Melatonin rises at night to help you wind down. Cortisol rises in the morning to help you wake up. But when blood sugar is unstable or cortisol is too high at night, it suppresses melatonin.

This is common in women with:

• Adrenal dysfunction
• Low calorie intake
• Reactive hypoglycemia
• Unmanaged stress or trauma
• Thyroid imbalance (especially poor conversion to T3)

Nighttime blood sugar crashes can spike cortisol, jolting you awake with a racing heart. Supporting steady blood sugar and calming the HPA axis helps restore your natural melatonin rhythm.

Why Melatonin Supplements Aren’t the Whole Answer

Melatonin supplements might help you fall asleep for a while, but they won’t solve the deeper problem if your body can’t make its own.

That’s why we look at the full picture:

• Are you getting enough tryptophan?
• Are you absorbing key nutrients?
• Are you balancing carbs and protein?
• What’s your cortisol doing at night?
• How’s your thyroid function?
• Are your mitochondria producing enough energy to fuel these conversions?

When we connect the dots, sleep gets easier—and deeper.

You Deserve to Wake Up Rested

If sleep has felt like a mystery, or like something that works for everyone else but not for you, you’re not broken.

You might just be missing the right raw materials. Or your thyroid might be under-functioning. Or your body might be trying to survive, not thrive.

This is where functional nutrition shines. Our team of dietitians takes your full story, labs, symptoms, and goals into account. Then we build a personalized plan that supports your sleep, metabolism, and hormone health from the inside out.

Not with gimmicks. Not with random supplements. But with clear, science-based strategies that restore your body’s natural rhythm.

Here are 5 action steps you can start with today:

1. Eat protein and complex carbs at dinner – this helps tryptophan get into your brain and sets the stage for melatonin production.
2. Create a calm bedtime routine – keep your room cool (around 68–69°F), avoid screens, dim the lights, and try reading a real book to help signal wind-down.
3. Support your morning cortisol rhythm – wake up around the same time daily, open the curtains, hydrate, get some light exposure (bonus for red light), and eat a balanced meal with protein, fat, and carbs.
4. Avoid overly restrictive diets – low-carb or low-calorie diets can disrupt both your thyroid and your sleep. Make sure you’re eating enough to fuel hormone and neurotransmitter production.
5. Look upstream – if you’ve tried all the surface-level fixes and still aren’t sleeping, it might be time to investigate your thyroid, nutrient status, gut health, and blood sugar patterns more deeply.

Ready to Dig Deeper?

If you’re tired of being tired and want to uncover what your body’s missing, we’re here to help.

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