The Connection Between Gut Health and Migraines

Daniel Gigante
Nov 22, 2025
3 min read

Learn how inflammation and gut imbalance may trigger headaches and migraines.

Migraines aren’t just “bad headaches.” They’re complex neurological events that can be triggered by everything from stress to sleep changes to — surprisingly — gut health. More and more research is uncovering a powerful link between the gut–brain axis and the onset of migraines, showing that digestive issues, inflammation, and microbiome imbalance may play key roles in who gets migraines and how severe they become.

Here’s what you need to know.

1. The Gut–Brain Axis: Your Internal Communication Highway

Your gut and brain constantly communicate through the vagus nerve, hormones, immune messengers, and even microbial metabolites. This relationship is called the gut–brain axis, and it explains why digestive problems can influence mood, pain perception, and even migraine activity.

When your gut is inflamed or out of balance, it sends distress signals to the brain — which can trigger neurological symptoms, including headaches.

2. Gut Imbalance Can Increase Systemic Inflammation

A disrupted microbiome (called dysbiosis) can allow harmful bacteria to thrive.

This imbalance may:

Increase intestinal permeability (“leaky gut”)
Allow inflammatory molecules to enter the bloodstream
Trigger immune responses that sensitize the brain
Increase production of cytokines linked to migraine pathways

People with chronic migraines often show higher inflammation markers and more digestive dysfunction than those who don’t.

3. GI Disorders and Migraines Commonly Overlap

Several gut-related conditions are strongly associated with migraines:

⭐ Irritable Bowel Syndrome (IBS)

Research shows people with IBS are at double the risk of developing migraines.

⭐ Celiac Disease & Gluten Sensitivity

Gluten-triggered gut inflammation can cause headaches in sensitive individuals.

⭐ H. pylori Infection

This stomach bacteria is connected to both migraines and chronic digestive inflammation.

⭐ GERD & Reflux

Acid imbalance and gut irritation may influence neurological symptoms.

If you struggle with both gut issues and migraines, you’re not alone — many patients experience the two together.

4. How Serotonin Links Digestion to Headaches

About 90% of your serotonin — a key neurotransmitter involved in mood, pain, and digestion — is made in the gut.

When the gut is inflamed or imbalanced, serotonin signaling becomes disrupted,

which can:

Alter pain thresholds
Influence blood vessels in the brain
Increase sensitivity to migraine triggers

This is one reason many migraine sufferers experience nausea, vomiting, or digestive changes during attacks.

5. Food Sensitivities Are a Major Gut–Migraine Trigger

Food-triggered migraines often start with gut inflammation rather than the food itself.

Common triggers include:

Dairy
Gluten
Processed meats (nitrates)
Artificial sweeteners
MSG
Alcohol
Caffeine fluctuations

Inflamed or imbalanced guts react more strongly to these ingredients.

6. How to Support Your Gut to Reduce Migraine Frequency

✔ Increase prebiotic fiber

Feeds good bacteria and improves microbiome diversity. Examples: asparagus, oats, bananas, garlic, flaxseed.

✔ Consider a high-quality probiotic

Some strains (like B. lactis, L. rhamnosus, and L. plantarum) may help regulate inflammation and digestion.

✔ Reduce highly inflammatory foods

Sugar, alcohol, fried foods, and processed snacks can worsen migraines.

✔ Support the gut lining

Ingredients like:

L-glutamine
Slippery elm
Marshmallow root
DGL licorice (GutGard®)

…can help soothe gut irritation.

✔ Track food triggers with a journal

Migraines often appear 12–48 hours after a trigger food — making patterns easy to miss unless tracked.

✔ Stay hydrated

Dehydration is both a gut stressor and a major migraine trigger.

7. When to Talk to a Doctor

See a provider if you have:

Migraines more than 4 times a month
New digestive symptoms
Chronic bloating, diarrhea, or constipation
Persistent nausea
Headaches linked to certain foods

A provider may recommend testing for:

Celiac disease
H. pylori
Food sensitivities
Gut dysbiosis
Nutrient deficiencies

Final Thoughts

Migraines are complex, but gut health plays a much bigger role than most people realize. By supporting your microbiome, reducing inflammation, and stabilizing digestion, many people experience fewer and less intense migraine episodes.

A healthier gut often means a calmer, more resilient brain.