Melatonin does not directly cause allergies, but in some people it can worsen allergy symptoms by increasing inflammation, making the nose more congested, or interacting with existing allergic rhinitis or asthma. A few studies suggest melatonin may also improve sleep during allergy season, which can indirectly help symptoms. Most reactions are mild or due to supplement additives — not melatonin itself. If symptoms worsen after taking melatonin, stop it and talk with an allergist.

Does Melatonin Help or Worsen Allergies? A Complete, Evidence-Based Guide

Millions of adults use melatonin to improve sleep, especially during allergy season when congestion, sneezing, and post-nasal drip make falling asleep difficult. But many people notice something confusing:

“My allergies feel worse after I take melatonin. Is it the melatonin — or something else?”

This guide breaks down what the science actually says, how melatonin interacts with allergic rhinitis and asthma, and when you should stop taking it or see a board-certified allergist.

Quick Answer

Melatonin does not treat allergies, but it can help some people sleep better during allergy flare-ups. In others, melatonin may increase nasal congestion or make nighttime allergy symptoms feel worse. The response varies by person.

Deep Guide

1. What Exactly Is Melatonin?

Melatonin is a hormone your brain produces at night to regulate sleep. Over-the-counter melatonin is a synthetic version used to improve:

• Trouble falling asleep
• Jet lag
• Shift work sleep issues
• Middle-of-the-night awakenings

It is not an antihistamine and has no direct anti-allergy effect.

2. Can Melatonin Trigger a Real “Allergic Reaction”?

True allergic reactions to melatonin are extremely rare.

What usually causes reactions:

• Fillers or additives
• Herbal blends combined with melatonin
• Dyes, flavorings, stabilizers
• Cross-contamination in manufacturing

Most reported allergy-like symptoms are due to these ingredients, not melatonin itself.

Symptoms that may come from supplement additives:

• Runny nose
• Sneezing
• Congestion
• Hives (rare)
• Upset stomach

If symptoms appear only with one brand, additives are the likely cause.

3. Can Melatonin Worsen Nasal Allergies or Asthma?

Yes — in some people.

Why this happens

Peer-reviewed studies show melatonin can affect inflammatory pathways and airway tone. For a subset of people, it may:

• Increase nasal blood flow
• Make nasal passages feel more “blocked”
• Increase nighttime coughing in asthma
• Increase awareness of congestion during sleep

The AAAAI notes that nighttime allergies worsen naturally because histamine levels rise overnight. Adding melatonin to an already congested airway may amplify that feeling.

Most common symptoms people report:

• Feeling “more stuffed up” after taking melatonin
• Waking up with sinus pressure
• More noticeable post-nasal drip
• Coughing at night

Not dangerous — but uncomfortable.

4. Can Melatonin Help Allergies Indirectly?

Yes. Melatonin improves sleep quality for some people, and better sleep can make allergy days easier.

Potential indirect benefits:

• More daytime energy
• Better immune regulation
• Less brain fog from sleep loss
• Reduced perception of allergy severity

Studies show melatonin may reduce oxidative stress, which can support the immune system in general — but this does not replace proper allergy treatment.

5. Why Nighttime Allergies Can Feel Worse Even Without Melatonin

Many people assume melatonin is the problem when the real issue is nighttime allergy triggers.

Common nighttime allergens:

• Bed dust mites
• Pillows and bedding allergens
• Bedroom mold
• Pets allowed in the bed
• High indoor humidity
• Late-day pollen exposure

Because symptoms worsen at night naturally, people often connect the dots incorrectly.

6. Should You Take Melatonin If You Have Allergic Rhinitis or Asthma?

You can — but it depends on your symptoms.

Below is a simple decision guide.

Melatonin & Allergies: Should You Use It?

7. Safe and Unsafe Ways to Use Melatonin If You Have Allergies

Safe uses

• Occasional short-term use
• Low dose (0.5–3 mg)
• Pure melatonin (avoid blends)
• Earlier in the evening

Avoid or stop melatonin if

• Congestion worsens
• You wake up coughing
• Asthma symptoms increase
• You experience facial swelling, hives, or trouble breathing (rare)

If any of these occur, stop immediately and see an allergist.

8. Does Melatonin Interact With Allergy Medications?

Melatonin has no known harmful interaction with:

• Antihistamines
• Nasal steroids
• Montelukast
• SLIT allergy drops
• Inhalers

(Referenced from AAAAI Ask-the-Expert and NIH data.)

But because melatonin may cause mild drowsiness, combining it with sedating antihistamines (e.g., diphenhydramine/Benadryl) can increase sedation.

9. Melatonin Is Not an Allergy Treatment — SLIT Is

While melatonin can help you sleep, only Sublingual Immunotherapy (SLIT) treats the root cause of allergies — the immune overreaction to allergens.

HeyAllergy’s SLIT program, HeyPak®, offers:

• Custom-formulated drops
• At-home treatment
• No shots, no weekly clinic visits
• Evidence-based safety (AAAAI/ACAAI guidelines)
• Long-term relief

Learn more: Allergy Drops (HeyPak®)

10. When to See an Allergist

See a board-certified allergist if:

• Nighttime symptoms disrupt sleep
• You feel worse after taking melatonin more than twice
• You wake up congested even outside pollen season
• You rely on sleep aids because allergies keep you awake
• You have uncontrolled allergic rhinitis or asthma
• You want long-term treatment (SLIT) instead of short-term symptom relief

You can meet a HeyAllergy allergist online at Book Appointment.

What To Do Next

Frequently Asked Questions (FAQ)

1. Can melatonin make allergies worse?
‍Yes, in some people melatonin increases nasal congestion or nighttime coughing. This is usually due to mild inflammatory effects or nighttime allergy flare-ups.

2. Can you be allergic to melatonin?
‍True melatonin allergy is extremely rare. Most reactions are caused by fillers, dyes, or herbal ingredients in supplements.

3. Does melatonin help with allergic rhinitis?
‍Melatonin does not treat allergies, but it can help improve sleep during allergy season. For allergy relief, treatments like nasal sprays, antihistamines, or SLIT drops work better.

4. Is melatonin safe if I have asthma?
‍Most people with asthma tolerate melatonin well, but if asthma symptoms worsen at night after taking it, stop and speak with an allergist.

5. What is the best long-term treatment for allergies?
‍Sublingual Immunotherapy (SLIT) allergy drops treat the root cause of allergies and provide long-term relief. Learn more at HeyPak®.

6. What should I take instead of melatonin if allergies keep me awake?
‍Try nasal steroid sprays, non-sedating antihistamines, saline rinses, or treating the root cause with SLIT. These directly reduce congestion that disrupts sleep.

‍

If melatonin is making your allergies worse — or if allergies disrupt your sleep — our board-certified allergists can help.
👉 Book your online consultation today: HeyAllergy.com/book-appointment

Author, Review & Disclaimer

Author: Krikor Manoukian, MD, FAAAI, FACAAI — Board-Certified Allergist/Immunologist
Bio: Dr. Manoukian is a board-certified allergist/immunologist specializing in telemedicine-enabled allergy care and personalized SLIT programs. He leads HeyAllergy’s clinical team and trains providers in safe immunotherapy.
Medical Review: HeyAllergy Clinical Team (Board-Certified Allergists/Immunologists)
Disclaimer: This article is educational and not a substitute for personalized medical advice. Always consult your clinician about your medications and treatment options.

References

• AAAAI — Ask the Expert, “No absolute contraindications” regarding medications and allergy immunotherapy.
• AAAAI/ACAAI — Sublingual Immunotherapy Practice Parameter Update (2017).
• NIAID/NIH — Immune response and airway inflammation research.
• Peer-reviewed studies on circadian rhythm hormones and airway inflammation.