How to Treat Reflux Naturally

GERD is one of the most common gastrointestinal diseases. The CDC states 20% of the US population struggles with GERD. Almost everyone will experience heartburn at some point, especially after a heavy meal. This is a common complaint here in Naples — the burning, pressure, or a sour taste creeping up the throat. Most assume it’s caused by too much stomach acid, but functional medicine research shows the opposite: most chronic reflux stems from low stomach acid, not high acid.

Here’s why:

Your lower esophageal sphincter (LES)—the “gate” between your esophagus and stomach—opens and closes based on pH levels. In a healthy digestive system, your stomach is very acidic. That acidity signals the LES to stay tightly closed.

But when stomach acid is too low (a condition called hypochlorhydria), the LES fails to close properly, allowing partially digested food and acids to bubble upward. That upward movement creates burning and pressure—symptoms that mimic “too much acid,” even though the real issue is not enough.

This is why over-the-counter drugs like Tums, PPIs, and acid blockers often offer temporary relief while making the underlying issue worse. They further reduce stomach acid, weakening the LES and impairing digestion even more. Over time, this can lead to nutrient deficiencies, poor protein absorption, increased bloating, and chronic reflux cycles.

At Harmony Health Clinic in Naples, we help patients restore normal digestion by reacidifying the stomach—a foundational step in functional medicine. One of the safest and most effective tools for this is Betaine HCl, a supplemental form of stomach acid that helps your body break down proteins, activate enzymes, absorb nutrients, and keep the LES closed properly.

Below is our official protocol:

Betaine HCl Challenge Protocol

Purpose: This self-guided assessment helps determine if your stomach acid levels are suboptimal.It should only be performed under professional supervision.

Step 1: Establish Your Starting Dose

Begin by taking one capsule of Betaine HCl (with pepsin, if available) with your largest protein-containing meal of the day. Swallow the capsule midway through your meal, not before or after.If you do NOT notice any warming, tingling, or burning in your stomach or chest after the meal, repeat the process the next day but increase to two capsules with the same type of meal.

Step 2: Gradual Increase

Continue increasing your dose by one capsule per day during your heaviest meal. You should increase until you experience a mild warming or burning sensation in your upper abdomen or throat, or reach a maximum of 8 capsules per meal without any sensation. A lack of response at higher doses suggests significantly low stomach acid production.

Step 3: Finding Your Maintenance Dose

When the warming sensation occurs, it indicates you’ve slightly exceeded your body’s need for acid support. The following day, reduce your dose by one capsule and continue taking that number with meals. Stay at that level until the warming sensation returns, then decrease by one more capsule. Continue adjusting downward in this stepwise manner until no discomfort occurs at your maintenance dose.

Step 4: Applying to All Meals

Once your optimal dose is found for your largest meal, you can scale the amount based on meal size:

• Large meals: full dose

• Medium meals: about half

• Small meals or snacks: 1–2 capsules

• Meals higher in protein or fat typically require more support, while lighter meals require less.

Step 5: Weaning and Reassessment

As digestion improves, your body may gradually restore normal stomach acid levels. If you consistently feel warmth or burning at your usual dose, reduce by one capsule and continue to reassess weekly.

Caution

• Never take Betaine HCl on an empty stomach.

• Do not use if you have active ulcers, gastritis, or are taking acid-suppressing medications (PPIs, H2 blockers).

• If discomfort persists after lowering your dose, stop the supplement and let us know—we can find an alternative approach. The end goal is to find the cause (i.e., H. pylori infection).

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Why Stomach Acid Matters for Your Whole Body

Healthy stomach acid levels are essential for:

• Breaking down proteins into absorbable amino acids

• Activating pepsin and other digestive enzymes

• Absorbing minerals like magnesium, iron, zinc, and B12

• Killing microbes and preventing infections (i.e. parasite infections)

• Ensuring proper gut motility

• Preventing gas, bloating, and fermentation in the small intestine

According to research from Harvard Health and the NIH, long-term use of acid-suppressing medications can increase risks for nutrient deficiency, pneumonia, C. diff, osteoporosis, and altered gut microbiome balance—all reasons many people seek natural care.

By reacidifying the stomach and correcting digestion, many patients in Naples report significant improvement in:

• Reflux and heartburn

• Bloating

• Gas and belching

• Early fullness

• Fatigue after meals

• Constipation or loose stools

• Food intolerances

When to Investigate the Root Cause

If reflux persists even with the Betaine HCl Challenge, deeper issues may be driving the dysfunction, including:

• H. pylori infection

• Small intestinal bacterial overgrowth (SIBO)

• Chronic stress and cortisol dysregulation

• Poor vagal nerve tone

• Low digestive enzyme output

• Gallbladder dysfunction

• Food sensitivities

• Autoimmune conditions

Our functional medicine team at Harmony Health Clinic can run advanced lab testing—including GI-MAP stool testing, H. pylori screening, nutrient panels, and digestive enzyme assessments—to identify your personal root cause and create a targeted treatment plan.

For severe reflux, long-term PPI use, or complicated digestion issues, we also offer telemedicine throughout Florida and in-office visits in Naples for comprehensive support.

Ready to Improve Digestion & Treat Reflux Naturally?

If you’re tired of relying on antacids or temporary relief, we can help you treat reflux naturally by addressing the root cause.

Schedule a visit with Harmony Health Clinic to evaluate your stomach acid, optimize digestion, and rebuild your gut health from the ground up.

Disclaimer: This article is for informational purposes only and does not constitute medical advice. Always consult with a licensed healthcare professional.