The Real Cause of Acid Reflux + How To Heal

Acid reflux, or gastroesophageal reflux disease (GERD, which is chronic acid reflux), is a major problem in the United States, where up to 20% of the population suffers from the burning, gnawing, burping, and other uncomfortable symptoms of acid above the stomach where it isn’t supposed to be. (1) 

In spite of how common it is, acid reflux remains largely misunderstood. There are several myths and misconceptions around what causes reflux, and the most common treatments often not only miss the underlying cause but create new problems. 

I hope my functional medicine take helps you better understand what’s really going on behind the scenes with heartburn, and how you can heal your gut without relying on long-term acid blocking medications. 

Defining Acid Reflux, GERD, and Heartburn 

Just a quick note on terminology before we get into it: 

Acid reflux occurs when some of the contents of your stomach, including stomach acid, backflow into your esophagus where they don’t belong. 

GERD, or gastroesophageal reflux disease, occurs when acid reflux becomes chronic (in order to be diagnosed with GERD, you need to experience acid reflux at least twice a week for several weeks). 

Heartburn is the classic symptom that we associate with acid reflux and GERD, which feels like a burning sensation in your chest or throat. 

Common Symptoms of GERD and Acid Reflux

In addition to the classic symptom, heartburn (which, for the record, not everyone experiences, as in the case of laryngopharyngeal reflux or “silent reflux”), reflux symptoms may include: (2)  

• Regurgitation of stomach contents (into mouth or throat) 
• Bloating 
• Excessive burping
• Nausea
• Upper abdominal or chest pain
• Difficulty or pain with swallowing 
• Chronic cough or throat clearing
• Hoarseness or inflammation of the vocal cords
• A sensation of a lump in the throat 

Symptoms may be worse after meals, when lying down, or during periods of high stress. 

Why We Need to Stop Blaming Stomach Acid 

It’s a common misconception that acid reflux is always caused by too much stomach acid. It can actually be brought on by high OR low stomach acid (both conditions can create the symptoms, which can be confusing), but with my patients at the telehealth functional medicine center I see low stomach acid way more often, and often among those who thought they had the opposite problem. 

What really causes acid reflux is, in most cases, lower esophageal sphincter (LES) dysfunction. The LES is a muscular valve that sits between the esophagus and the stomach. (3) Its job is to open selectively to let food pass into the stomach, then close tightly to keep stomach contents from flowing backward. 

When the LES weakens, loses its tone, or opens at the wrong time, reflux occurs, regardless of whether stomach acid is high or low. So what’s interfering with normal LES function? 

There are several factors that can weaken the tone of the sphincter, including lying down shortly after meals, eating in excess, drinking alcohol, chewing inadequately, hiatal hernias, and increased intra-abdominal pressure usually brought on by obesity. 

One major factor that can disrupt LES function is low stomach acid, or hypochlorhydria. We need sufficient stomach acid in order for the feedback mechanism involved in closing the LES to work. When stomach acid is too low, the sphincter can become too relaxed and allow stomach contents to backflow into the esophagus. 

I think where many people get confused is that the symptoms of acid reflux do occur as a result of there being stomach acid in the esophagus. On the surface, the simplest solution is to get rid of the acid. But when you understand the mechanisms behind it, you can see that the acid itself isn’t the problem. More importantly, we need sufficient stomach acid to digest our food, absorb nutrients, and protect the health of our guts overall. 

Underlying Causes of Acid Reflux and GERD 

As we just started to explore, acid reflux and GERD are usually brought on by LES dysfunction. But as we understand in functional medicine, there’s always a cause beneath the cause. In most cases, this is a downstream effect of multiple overlapping imbalances rather than one single factor. 

Here are some of the most common underlying causes and contributing factors. 

Intra-Abdominal Pressure

Increased pressure within the abdomen can physically push stomach contents upward against the LES. This pressure may be driven by bloating and gas; overeating or eating large meals; obesity or being overweight (particularly excess weight around the midsection); constipation; or delayed gastric emptying. This can also occur during pregnancy. 

Low Stomach Acid (Hypochlorydia) 

Adequate stomach acid is essential for breaking down protein, triggering digestive enzyme release, absorbing key nutrients including magnesium, zinc, iron, and vitamin B12, and keeping gut bacteria levels in check. When stomach acid is too low, food isn’t digested efficiently. This can lead to fermentation, gas production, and bloating, which increases intra-abdominal pressure and prevents the LES from closing properly. 

As I mentioned above, low stomach acid also weakens signaling at the sphincter, which can also keep it from closing tightly. 

Our Western diet, food intolerances, medications, chronic infections, environmental toxins, and chronic stress can all contribute to low stomach acid. 

Gut Dysbiosis and SIBO 

An imbalanced gut microbiome, including bacterial overgrowth in the small intestine (SIBO), can significantly contribute to reflux symptoms. Excess gas production increases pressure in the digestive tract, while inflammation can disrupt normal motility and sphincter function. Low stomach acid can also contribute to SIBO. 

Chronic Stress and Nervous System Imbalance 

In order to properly produce and release digestive fluids including stomach acid, and properly digest our food, we need to be in a parasympathetic (“rest and digest”) state when we’re eating. Chronic stress, as well as acute stress, can keep the body in a sympathetic (“fight or flight”) state when eating, reducing stomach acid (HCl) production, slowing motility, and impairing coordination of digestive muscles including the LES. Anxiety has also been linked to GERD. (4) 

High Stomach Acid 

While less common in my experience, some people do produce excess acid, often in response to inflammatory diets, delayed stomach emptying, or certain kinds of infection. High acid can directly irritate the esophagus. Of course, the challenge is that both high and low stomach acid symptoms can feel the same, which is part of why guessing, or suppressing acid indefinitely, can backfire. 

Trigger Foods and Food Sensitivities 

Some of the most common trigger foods for reflux are fried foods, spicy foods, tomatoes, citrus fruits, alcohol, caffeine, and ultra-processed foods. Unless you’re eating a high volume of these foods in your diet (which may happen in a standard American diet), these foods are unlikely to cause a reflux problem on their own, but they can definitely exacerbate symptoms of an existing issue. 

In other cases, more subtle food sensitivities may contribute to the greater digestive issues that often underlie reflux. Sensitivities to gluten, dairy, or other foods can drive inflammation and reflux. 

READ MORE: 13 Inflammatory Foods You Need To Ditch Now, According To A Functional Medicine Expert 

Other Triggers and Risk Factors 

There are several other factors that can contribute to reflux, exacerbate or trigger symptoms, or predispose individuals to an increased risk of GERD. These include: 

• Hiatal hernia 
• Connective tissue disorders including scleroderma 
• Low levels of zinc (required for HCl secretion) or magnesium (required for LES muscle control) 
• Eating right before bed 
• Eating when already full 
• Use of certain medications including antidepressants, NSAIDs, PPIs (yes, the exact medications most commonly prescribed for GERD), anticholinergic medications, and calcium channel blockers 
• Age (stomach acid levels naturally decline over time) 

How To Determine Your Root Cause

The underlying picture of acid reflux is different for everyone. That’s why a comprehensive functional medicine health history and diagnostic testing can uncover the underlying culprit for individual cases. 

I often do specialized testing which may include comprehensive gut microbiome analysis, SIBO testing, food sensitivity testing, micronutrient testing, and others in order to get at the root cause of GERD. 

The key is to get to that root cause, and not to just suppress symptoms with an acid blocker, which often makes things worse. Of course, I’m not saying this to shame anyone who has been prescribed or is taking one of these medications. But hopefully the information I’m sharing here can help you make the right decision for you, ideally with a trusted healthcare provider, about how to move forward and heal your digestive system holistically. 

Risks of Long-Term PPI Use

Conventional practitioners usually prescribe acid blockers, including H2 blockers or proton pump inhibitors (PPIs), for GERD. Common PPIs include omeprazole (Prilosec) and lansoprazole (Prevacid). They work by suppressing the stomach acid production, which is required for digestion, nutrient absorption, and immune system function. 

Acid reducing medications can relieve symptoms, but they often create more significant problems, especially with long-term use. They are actually not meant to be used long-term, but the standard in clinical practice in the United States is to prescribe them indefinitely. 

Research has linked prolonged PPI use to: 

• Nutrient deficiencies (magnesium, calcium, iron, vitamin B12) (5) 
• Increased risk of bone fractures and osteoporosis (6) 
• Gut dysbiosis and increased risk of SIBO (7) 
• Low stomach acid (which has been associated with leaky gut and autoimmune conditions)
• Higher susceptibility to infections
• Potential kidney and cardiovascular concerns (8, 9) 
• Increased risk of cancer (10) 
• Increased risk of inflammatory bowel disease (IBD) 

And, of course, PPIs do not address the root cause of reflux. They reduce symptoms while often perpetuating the underlying imbalance. 

If PPIs reduce symptoms, practitioners will generally say that they “work”. Yes, they might work, in the same way that turning off the water works when the pipe under the sink is leaking. But that’s not a solution—we have to fix the leak, and importantly, figure out why it occurred in the first place. 

Functional Medicine Treatment Options

There are a number of effective natural solutions and lifestyle changes that can help heal your digestive tract and LES, and encourage good overall digestive health going forward:

• Identify the root cause of your reflux. Okay, I know I’ve already made this point, but it’s worth repeating because getting to the root cause is really the key to healing. 
• Consult with a practitioner about supplemental HCl. If you have low stomach acid, taking supplemental hydrochloric acid (HCl) with meals can help while you work on restoring natural production. I recommend working with a functional medicine practitioner to determine if, and how much, you should try. Digestive enzymes can also be helpful while you’re working on healing your gastrointestinal system. You can try my blend of digestive enzymes + HCl here. 
• Eat an anti-inflammatory diet. Food is foundational, and everything you eat has the power to either heal or disrupt your gut. 
• Eat fermented foods. Fermented foods like kimchi, sauerkraut, kvass, and kombucha can help to restore and rebalance your body’s beneficial bacteria levels, so consider bringing more of these into your diet.
• Identify and remove triggers. Reduce alcohol, caffeine, late night meals, and consider cutting back on large meals (just make sure you’re still eating enough food). An elimination diet can also help you identify hidden food sensitivities that may be behind your symptoms. 
• Try digestive bitters. Bitter herbs and foods consumed at the beginning of meals can help naturally stimulate digestion and the secretion of fluids like stomach acid. I love dandelion, burdock root, and bitter melon. 
• Heal your gut lining. Soothing nutrients and supplements often used in functional medicine include deglycyrrhizinated licorice (DGL); zinc carnosine; aloe vera; and l-glutamine. My blend GI Calm includes several of these ingredients. 
• Consider healthy weight loss. This isn’t relevant in all cases, but if you are experiencing GERD alongside obesity or overweight, losing weight, especially fat around your belly, can make a huge difference in your reflux symptoms and overall digestive health. (11) 
• Restore microbiome balance. Probiotics help to restore the balance in the gut microbiome, and may help to improve GERD symptoms. (12) 
• Regulate the nervous system. Diaphragmatic breathing before meals can help to bring you into the rest and digest state. (13) Mindfulness practices and improving sleep hygiene can help with overall stress levels. 

Every person is different, so a “one-size-fits-all” approach is inadequate to say the least. However, whatever the reason, chances are that acid-suppressing medication is not the solution! Functional medicine can help you to pinpoint your individual health picture.

A Functional Medicine Approach to Acid Reflux

Acid reflux is almost always more than just an acid problem. It’s your body telling you that digestion, motility, microbiome balance, or nervous system regulation is off.

While medications may offer temporary symptom relief, lasting healing comes from understanding and addressing the root cause. We can help you find the right functional medicine approach and treatment plan. 

Read Next: 11 Surprising Ways Slippery Elm Can Level Up Your Health

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. 

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Sources

• Gastroesophageal reflux disease (GERD) Mayo Clinic 
• Richter, J. E., & Rubenstein, J. H. (2018). Presentation and epidemiology of gastroesophageal reflux disease. Gastroenterology, 154(2), 267-276.
• Rosen, R. D., & Winters, R. (2023). Physiology, lower esophageal sphincter. In StatPearls [Internet]. StatPearls Publishing.
• Henning, M., Lindgen, K., Paul, D., Fuchs, C., Niecke, A., Albus, C., … & Leers, J. (2024). Association between anxiety and reflux symptoms in patients with gastroesophageal reflux disease: A prospective cohort study. Cureus, 16(11).
• Lehault, L. W. B., & Hughes, D. M. (2017). Review of the long-term effects of proton pump inhibitors. Federal Practitioner, 34(2), 19.
• Yang, J., Zhou, T. J., Yang, J., & Bao, D. N. (2022). Use of acid-suppressive drugs and risk of fracture in children and young adults: a meta-analysis of observational studies. European Journal of Clinical Pharmacology, 78(3), 365-373.
• Zhang, J., Zhang, C., Zhang, Q., Yu, L., Chen, W., Xue, Y., & Zhai, Q. (2023). Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota. BMC microbiology, 23(1), 171.
• Wu, C. C., Liao, M. H., Kung, W. M., & Wang, Y. C. (2023). Proton pump inhibitors and risk of chronic kidney disease: evidence from observational studies. Journal of Clinical Medicine, 12(6), 2262.
• Kim, S. Y., & Lee, K. J. (2024). Potential risks associated with long-term use of proton pump inhibitors and the maintenance treatment modality for patients with mild gastroesophageal reflux disease. Journal of neurogastroenterology and motility, 30(4), 407.
• Sawaid, I. O., & Samson, A. O. (2024). Proton pump inhibitors and cancer risk: a comprehensive review of epidemiological and mechanistic evidence. Journal of clinical medicine, 13(7), 1970.
• Jacobson, B. C., Somers, S. C., Fuchs, C. S., Kelly, C. P., & Camargo Jr, C. A. (2006). Body-mass index and symptoms of gastroesophageal reflux in women. New England Journal of Medicine, 354(22), 2340-2348.
• Cheng, J., & Ouwehand, A. C. (2020). Gastroesophageal reflux disease and probiotics: a systematic review. Nutrients, 12(1), 132.
• Qiu, K., Wang, J., Chen, B., Wang, H., & Ma, C. (2020). The effect of breathing exercises on patients with GERD: a meta-analysis. Annals of palliative medicine, 9(2), 40513-40413.