Migraines and Headaches: A Functional Medicine Deep Dive Into Gut, Liver, and Hormonal Root Causes
Migraines and chronic headaches aren’t just inconvenient —they’re often a sign that your body is out of balance. While conventional medicine typically treats migraines with painkillers or triptans, functional medicine asks a deeper question: why is this happening in the first place?
Emerging research points to root causes such as gut health issues, nutrient deficiencies, liver congestion, hormonal imbalances, and neurotransmitter disruptions as being closely linked to chronic headaches and migraines. Let’s explore these connections — and how to begin healing from the inside out.
Jump to Section
- Gut Dysbiosis and Leaky Gut
- Low Stomach Acid and Mineral Deficiencies
- What Causes Low Stomach Acid?
- Electrolyte Imbalance
- Lemon Water with Sea Salt
- Liver Congestion and Detox Issues
- Hormonal Imbalance
- GABA and Neurotransmitter Imbalance
- Common Migraine Triggers
- Functional Testing
- Functional Medicine Protocol
- Healing Foods & Foods to Avoid
- Final Thoughts
Root Cause 1: Gut Dysbiosis and Leaky Gut
Your gut isn’t just for digestion—it’s your second brain. Studies now show that individuals with migraines often have imbalanced gut microbiota, also known as gut dysbiosis.
What Does "Imbalanced Gut Microbiota" Mean?
Gut dysbiosis refers to a disruption in the normal balance of bacteria, fungi, viruses, and other microbes in your gastrointestinal tract—particularly the colon. This imbalance may include:
- Overgrowth of harmful microbes
- Decline in beneficial bacteria
- Reduced microbial diversity
What Is Gut Microbiota?
The gut microbiota is composed of trillions of microbes—primarily beneficial bacteria that:
- Aid in digestion
- Regulate immune function
- Produce vitamins (e.g., B12, K, folate)
- Generate neurotransmitters (e.g., serotonin, GABA)
- Protect the gut lining from pathogens
A 2020 study published in Nature Reviews Neurology found that gut-brain axis dysfunction is strongly correlated with migraine development (source).
How It Affects You:
- Overgrowth of harmful bacteria releases endotoxins, triggering systemic inflammation.
- A “leaky” gut allows toxins and partially digested proteins to enter the bloodstream, activating the immune system and leading to inflammatory responses in the brain.
Root Cause 2: Low Stomach Acid and Mineral Deficiencies
Many individuals with chronic migraines also suffer from hypochlorhydria—low stomach acid. This impairs your ability to:
- Absorb essential minerals like magnesium, zinc, B12, and iron
- Break down proteins into amino acids like tryptophan (needed for serotonin production)
- Prevent microbial overgrowth in the digestive tract
A 2019 clinical review in Nutrients confirms that magnesium deficiency is linked to the severity and frequency of migraines (source).
What Causes Low Stomach Acid?
A Functional Medicine BreakdownLow stomach acid (hypochlorhydria) is more common than most people realize. It plays a critical role in digestion, nutrient absorption, and defense against pathogens. When stomach acid is too low, a cascade of issues can follow—including bloating, malabsorption, acid reflux, and chronic inflammation.
1. Medications: PPIs and Antacids
Proton pump inhibitors (PPIs) and H2 blockers are commonly prescribed for GERD and ulcers, but they directly suppress hydrochloric acid. Long-term use increases the risk of nutrient deficiencies, bacterial overgrowth, and digestive complications.
- Can cause magnesium, B12, and iron deficiencies
- Linked to SIBO and C. difficile infection
PubMed: Acid suppression and nutrient malabsorption
2. Aging
Stomach acid production naturally declines with age. By age 60, many individuals experience hypochlorhydria, increasing the risk of poor digestion and bacterial overgrowth.
Study: Age-related hypochlorhydria prevalence (Gut Journal)
3. H. pylori Infection
Helicobacter pylori is a common stomach bacterium that suppresses acid production and damages parietal cells. It is one of the top infectious causes of low stomach acid and atrophic gastritis.
NIH: H. pylori and gastric function
4. Chronic Stress and Vagus Nerve Dysfunction
The vagus nerve helps regulate stomach acid through parasympathetic activation. Chronic stress, trauma, or poor vagal tone can lead to low acid output and sluggish digestion.
Frontiers in Psychiatry: Stress and digestion
5. SIBO (Small Intestinal Bacterial Overgrowth)
Low stomach acid allows bacteria to bypass stomach defenses and colonize the small intestine, contributing to SIBO. The bacterial overgrowth further impairs digestion and feedback loops.
6. GERD (Reflux)
Contrary to common belief, GERD often stems from too little stomach acid, not too much. Insufficient acid means food isn’t broken down properly, causing gas, pressure, and backflow into the esophagus.
Annals of Gastroenterology: GERD and low acid
7. Poor Eating Habits
Eating quickly, under stress, or skipping meals disrupts natural digestive signaling. Improper chewing or excessive water with meals can dilute or delay acid secretion.
8. Sedentary Lifestyle and Poor Posture
A lack of movement and poor posture reduces vagal tone, lymphatic circulation, and digestive flow. Lying down after eating can worsen gastric pressure and digestion.
Research published in the journal Clinical Nutrition Research confirms that electrolyte and mineral imbalances can impair digestion and acid production.
Electrolyte Deficiencies That Can Impact Stomach Acid
- Low chloride, which is found in salt (sodium chloride), is essential for the production of hydrochloric acid (HCl).
- Low magnesium: Reduces energy for acid production and impairs enzyme function.
- Low potassium: Affects electrolyte gradients and parietal cell function.
- Dehydration: Concentrates or dilutes electrolytes, reducing digestive secretions.
Electrolyte Imbalance
- Fatigue, muscle cramps, or irregular heartbeat
- Dry mouth, thirst, or poor saliva production
- Constipation or slow digestion
- Low stomach acid symptoms like bloating, burping, or reflux
How to Replenish Electrolytes Naturally
- Unrefined sea salt or Himalayan salt (rich in sodium and trace minerals)
- Coconut water or electrolyte powders without added sugars
- Dark leafy greens, avocado, bananas, and mineral-rich broths
- Magnesium glycinate or citrate supplements if deficient
Can Lemon Water with Sea Salt Act as an Electrolyte Drink?
Yes! A simple mix of lemon juice, filtered water, and a pinch of unrefined sea salt can function as a natural electrolyte drink. It’s a gentle, everyday way to replenish key minerals and support hydration, digestion, and even stomach acid production.
How It Works:
| Ingredient | Benefit | Electrolytes Provided |
|---|---|---|
| Lemon juice | Provides potassium and vitamin C | Small amounts of potassium |
| Unrefined sea salt | Supplies essential minerals | Sodium, chloride, magnesium, calcium |
| Filtered water | Supports hydration and mineral absorption | Helps deliver electrolytes throughout the body |
Key Electrolytes Supported:
- Sodium & Chloride: From sea salt—crucial for hydration and stomach acid production (HCl).
- Potassium: From lemon—supports nerve function and muscle health.
- Magnesium & Calcium: Found in trace amounts in quality sea salt—help with energy and enzyme function.
Tips for Best Results:
- Use Himalayan pink salt or Celtic sea salt, not processed table salt.
- Drink it first thing in the morning or 15–20 minutes before meals to support digestion.
- Not a substitute for medical-grade electrolyte solutions, but excellent for everyday support.
Supported by Research:
- PubMed: Electrolyte-enhanced water and cellular hydration
- NIH: Sodium, chloride, and gastric acid secretion
This natural electrolyte mix also supports your digestive health—making it a smart and functional wellness tool.
9. Autoimmune Gastritis and Pernicious Anemia
Autoimmune conditions can damage parietal cells—the cells that produce both hydrochloric acid and intrinsic factor. Over time, this can result in complete loss of acid production and B12 deficiency.
Mayo Clinic: Pernicious anemia and gastric atrophy
Summary Table: What Causes Low Stomach Acid?
| Cause | Mechanism |
|---|---|
| PPIs and antacids | Suppress acid production directly |
| Aging | Natural decline in acid-producing cells |
| H. pylori infection | Disrupts acid-producing parietal cells |
| Chronic stress | Inhibits vagus nerve and gastric stimulation |
| SIBO | Bacterial overgrowth interferes with digestion |
| GERD | Reflux due to incomplete digestion and low acid |
| Poor eating habits | Inhibit digestive signals and enzyme secretion |
| Sedentary lifestyle | Reduces motility and vagal stimulation |
| Autoimmune gastritis | Destroys acid-producing cells in the stomach |
Need help restoring your stomach acid naturally? Functional testing and lifestyle protocols can help identify the root causes. Reach out or explore our wellness blog for more guides.
Root Cause 3: Liver Congestion and Detox Issues
The liver is your body’s main detox organ—processing hormones, environmental toxins, food additives, and medications. When the liver becomes sluggish or overburdened, toxins recirculate, often triggering headaches and migraines.
Additionally, poor bile flow and impaired phase II liver detox can lead to
- Estrogen dominance
- Histamine buildup
- Accumulation of metabolic waste
Functional medicine often finds impaired methylation and glutathione detox pathways in individuals who suffer from migraines.
Root Cause 4: Hormonal Imbalance
Hormonal fluctuations—especially the estrogen drop before menstruation—are a major migraine trigger in women.
According to the Journal of Headache and Pain, hormonal migraines are associated with
- Estrogen dominance
- Low progesterone
- Poor liver metabolism of estrogen
Root Cause 5: GABA and Neurotransmitter Imbalance
GABA (gamma-aminobutyric acid) is your brain’s calming neurotransmitter. Low levels of GABA can lead to anxiety, tension, and migraine-like pain.
Gut dysfunction and poor protein digestion reduce GABA synthesis. Other contributing factors include
- Low vitamin B6
- Chronic stress
- Gut dysbiosis (especially loss of bacteria like Lactobacillus rhamnosus)
A 2022 study in Frontiers in Neurology found that low GABA activity is associated with increased migraine sensitivity and altered pain perception (source).
Common Migraine Triggers—and What They Indicate
| Trigger | What It Suggests |
|---|---|
| Processed foods, MSG, nitrates | Liver detox burden |
| Hormonal cycles | Estrogen/progesterone imbalance |
| Sleep disturbances | GABA/serotonin dysregulation |
| Chronic stress | Cortisol imbalance, adrenal strain |
| Gut discomfort or bloating | Dysbiosis, leaky gut, low stomach acid |
Functional Medicine Testing to Consider
- GI Map or GI Effects: Assesses dysbiosis, leaky gut, parasites
- DUTCH Test: Reveals hormone levels, estrogen metabolism, cortisol patterns
- Organic Acids Test (OAT): Evaluates B-vitamin status, mitochondrial health, neurotransmitter markers
- Hair Tissue Mineral Analysis (HTMA): Detects mineral imbalances (magnesium, zinc, copper)
Functional Medicine Protocol for Migraine Relief
1. Heal the Gut
- L-glutamine, marshmallow root, slippery elm soothe and repair gut lining
- Probiotics: Lactobacillus plantarum, Bifidobacterium longum
- Digestive enzymes + HCl—support digestion and nutrient absorption
2. Support the Liver
- Milk thistle, burdock root, dandelion— enhance detoxification
- Liposomal glutathione— supports phase II liver detox
- Castor oil packs—apply over liver at night
3. Replenish Key Nutrients
- Magnesium glycinate or threonate—400–600 mg/day
- Vitamin B6 (P5P) – 25–50 mg/day
- Riboflavin (B2)—200–400 mg/day
- Omega-3s (DHA/EPA) – reduce inflammation
4. Balance Hormones Naturally
- Chaste tree berry (Vitex)—supports progesterone
- DIM or calcium D-glucarate—helps detoxify estrogen
- Maca root—adaptogenic support for hormonal balance
5. Calm the Nervous System
- L-theanine, GABA, taurine – promote relaxation
- Ashwagandha or holy basil – support adrenal health
- Magnesium and lavender oil – promote restful sleep
Foods That Support Healing & Foods to Avoid
- Leafy greens (magnesium, folate)
- Beets and carrots (liver support)
- Bone broth (gut lining and minerals)
- Wild salmon, sardines (omega-3s)
- Fermented foods (probiotics)
Foods to Avoid
- Gluten and dairy (can worsen leaky gut)
- Sugar and refined carbs (trigger inflammation)
- Alcohol (liver stress, histamine release)
- Soy (may disrupt hormonal balance)
Final Thoughts
Migraines are not just in your head — they are often signs of deeper systemic imbalances. Functional medicine empowers you to find the root causes and treat the entire body, not just the symptoms.
By restoring gut health, supporting liver detox, correcting nutrient deficiencies, and balancing hormones and neurotransmitters, lasting relief is possible.
Want to Heal Your Gut?
Healing the gut lining and correcting dysbiosis is essential for long-term improvement.
To dive deeper into how to repair a leaky gut and rebalance your microbiome, don’t miss our in-depth blog:
Leaky Gut & Dysbiosis: The Hidden Gut Imbalances Behind Fatigue, Brain Fog, and Inflammation
It covers the root causes, symptoms, functional medicine protocols, and the most effective herbal and nutritional tools to help you begin healing your gut—naturally and thoroughly.
About the Author
Written by Delilah Ko, a functional medicine student passionate about uncovering the root causes of chronic conditions. Delilah combines science-backed research with holistic insights to make complex health topics accessible and empowering.
Disclaimer:
This blog is written by a student currently studying functional medicine and is intended for educational and informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment. Always consult your healthcare provider before starting any new supplement or protocol, especially if you have an underlying medical condition or are taking medications.
