Why Acid Reflux Happens: The 4 Root Causes Doctors Often Miss

Tiffany Wooten
Nov 3
3 min read

You feel the familiar burn in your chest and wonder, "Why is this happening to me again?" If you think the answer is simply "spicy food" or "too much stomach acid," you're only seeing the tip of the iceberg.

A woman holding her chest with eyes closed, looking into the sun, taking a deep breath.

Understanding why acid reflux happens is the most powerful step you can take toward stopping it for good. True healing begins when we look beyond the symptoms and identify the underlying root causes that conventional medicine often overlooks.

Based on a functional medicine approach, here are the 4 primary reasons why acid reflux happens and what’s really going on inside your body.

1. Low Stomach Acid (The "Slow Digester")

What Happens: Contrary to popular belief, many cases of reflux are caused by too little stomach acid (Hypochlorhydria), not too much. Stomach acid is essential for digesting food and signaling the valve at the top of your stomach (the LES) to close tightly. When acid is low, food sits and ferments, creating gas. This pressure pushes the little acid you have upward.

Common Signs: Bloating shortly after meals, undigested food in stool, nutrient deficiencies, and a feeling of heavy fullness.

What to Do Next: If this sounds familiar, our guide dives deep into dietary shifts and safe testing methods to support healthy acid levels.

2. Gut Dysbiosis & SIBO (The "Gas Factory")

What Happens: An overgrowth of bacteria in your small intestine (SIBO) or an imbalance in your gut microbiome (dysbiosis) can be a primary driver of reflux. These bacteria ferment carbohydrates from your food, producing significant amounts of gas. This gas creates intra-abdominal pressure that physically forces stomach contents into the esophagus.

Common Signs: Bloating that worsens as the day goes on, excessive gas, food intolerances (especially to FODMAPs), and altered bowel habits.

What to Do Next: This complex cause requires a specific approach. Learn more about the gut-reflux connection in this article from Healthline: What Is SIBO?, and then discover our targeted protocol inside our comprehensive guide.

3. Stress & Poor Motility (The "Stressed-Out System")

What Happens: Your gut and brain are in constant communication via the vagus nerve. Chronic stress puts your nervous system in "fight-or-flight" mode, which directly slows digestion, relaxes the esophageal valve (LES), and can reduce stomach acid production. This perfect storm allows acid to back up easily.

Common Signs: Reflux that flares during stressful periods, a "lump in the throat" sensation (globus), anxiety, and poor sleep.

What to Do Next: Managing stress is not a luxury; it's a necessity for gut health. The American Institute of Stress explains the science behind this link, and our guide provides a practical playbook for calming your nervous system to calm your gut.

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4. Structural Issues & Direct Triggers (The "Faulty Gate")

What Happens: Sometimes, the cause is more direct. A hiatal hernia (where the stomach pushes through the diaphragm) can mechanically disrupt the LES. Additionally, certain foods and medications can be direct triggers. For example, caffeine and alcohol can chemically relax the valve, while NSAIDs (e.g., ibuprofen) can irritate the gut lining.

Common Signs: Symptoms immediately after specific trigger foods, pain when bending over or lying down, and reflux that began or worsened with certain medications.

What to Do Next: Identifying and managing these triggers is a key part of the solution, which we outline in detail in our ultimate Guide to Acid Reflux.