Acid Reflux and Heartburn: Why Antacids Are Not the Answer and What to Do Instead
By Joana Amram, Registered Nutritional Therapist & Naturopath (ANP)· Lisbon, Portugal
Acid reflux is one of those conditions where the standard treatment and the actual root cause are so misaligned that the treatment frequently makes the underlying problem worse over time.
Millions of people take proton pump inhibitors or antacids daily — sometimes for years, sometimes for decades — to manage heartburn and reflux symptoms. Many of them find that if they try to stop, the symptoms return, often worse than before. This rebound effect is not coincidence. It is a direct consequence of what the medication does to stomach acid physiology.
Understanding what is actually driving reflux — which is rarely what most people assume — changes the entire approach to treating it.
What Reflux Actually Is
Acid reflux occurs when stomach contents move upward from the stomach into the oesophagus. The burning sensation — heartburn — is caused by stomach acid making contact with the oesophageal lining, which unlike the stomach is not protected against acid.
The mechanism that normally prevents this from happening is the lower oesophageal sphincter (LOS) — a muscular valve at the junction between the oesophagus and stomach that opens to allow food in and then closes tightly to keep stomach contents down.
When reflux occurs, it is because that valve has opened when it should not have. The central question — one that is rarely asked in a standard clinical consultation — is why is the valve opening?
The Low Stomach Acid Paradox
Here is the most important and counterintuitive thing about acid reflux: in the majority of people who experience it, the problem is not too much acid. It is too little.
This sounds impossible. The burning sensation is vivid and real. But the sensation is caused by acid in the wrong place — not by excess acid in the stomach. The distinction matters enormously.
When stomach acid levels are adequate, several things happen correctly. Food is broken down efficiently in the stomach. The stomach empties at the right pace. The pyloric valve — which connects the stomach to the small intestine — opens in response to the correct acid signal. The lower oesophageal sphincter, which responds to the pressure and chemistry of a properly functioning stomach, stays closed.
When stomach acid is low, food sits in the stomach for longer because the gastric emptying signal is weaker. That food ferments. Fermentation produces gas. Gas creates upward pressure. That pressure forces the lower oesophageal sphincter open. Acid — even a small amount — rises into the oesophagus and burns.
The acid that burns is not excess acid. It is normal or below-normal acid in the wrong location, driven upward by pressure from fermentation.
This mechanism explains something many reflux sufferers notice: their symptoms are not necessarily correlated with "acidic" foods. They occur after large carbohydrate-heavy meals, after eating quickly, or in the hours after eating — all situations consistent with slow gastric emptying and fermentation rather than acid overproduction.
Why Antacids and PPIs Create Dependency
Proton pump inhibitors (PPIs) — omeprazole, lansoprazole, esomeprazole — work by blocking the proton pumps in the stomach lining that produce acid. Antacids work by neutralising acid directly.
Both approaches reduce the symptom. Neither addresses the cause. And both, with long-term use, create physiological changes that make the underlying problem harder to resolve.
When stomach acid is suppressed, gastric emptying slows further. The microbiome of the stomach and upper gut shifts — acid-suppression allows bacteria that would normally be killed to survive and proliferate in the upper digestive tract, increasing the fermentation and gas production that drives reflux. The body, sensing low acid, upregulates the number of acid-producing cells (a process called hypergastrinaemia). When the medication is stopped, those extra cells produce a surge of acid — the rebound reflux that makes stopping PPIs so difficult.
This is not a reason to stop PPIs abruptly or without support — rebound reflux can be severe and oesophageal health matters. It is a reason to understand that long-term PPI use does not solve the problem and creates its own complications, and to work with a practitioner who can support a structured withdrawal process alongside root-cause treatment.
Long-term PPI use is associated with: increased risk of gut infections (particularly Clostridioides difficile and SIBO), reduced absorption of magnesium, B12, calcium, and iron, and an increased fracture risk in older adults. These are not reasons to panic if you take them — they are reasons to take the root cause seriously.
Other Causes of Reflux Worth Investigating
Low stomach acid and fermentation pressure are the most common drivers of functional reflux, but they are not the only ones.
Hiatus Hernia
A hiatus hernia occurs when part of the stomach pushes up through the diaphragm into the chest cavity. This mechanically weakens the lower oesophageal sphincter and makes reflux more likely regardless of stomach acid levels. Hiatus hernias are common — many are asymptomatic — but they can be a significant contributor to reflux that does not respond to standard approaches. Diaphragmatic breathing exercises and specific dietary adjustments can help; in significant cases surgical management is appropriate.
SIBO
Small intestinal bacterial overgrowth creates excess gas and fermentation in the small intestine, producing upward pressure that contributes to reflux. Many people with chronic reflux — particularly those who also have bloating, IBS symptoms, or post-meal fatigue — have SIBO as an underlying driver. Treating the SIBO relieves not just digestive symptoms but often resolves or significantly reduces the reflux.
Helicobacter Pylori
H. pylori is a bacterial infection in the stomach lining that affects approximately 44% of the global population, many of whom are asymptomatic. It can cause gastritis and ulcers, and is associated with both reflux and paradoxically with low stomach acid (it disrupts acid-producing cells). Testing and treating H. pylori where present is an important part of a thorough reflux assessment.
Eating Habits and Meal Timing
How and when you eat is often more impactful on reflux than what you eat. The most clinically significant habits include:
Eating too quickly. Rapid eating means larger food particles, more air swallowed, less digestive enzyme activation, and faster stomach filling — all of which increase reflux risk.
Eating large meals. Volume in the stomach increases pressure on the lower oesophageal sphincter. Smaller, more frequent meals (not snacks — proper small meals) can reduce this.
Eating close to lying down. Gravity assists gastric emptying and keeps stomach contents down. Lying down within 2–3 hours of eating removes that assistance. Elevating the head of the bed slightly can help people with nocturnal reflux.
High-fat meals. Fat slows gastric emptying significantly, increasing the window during which fermentation and pressure can build. This does not mean avoiding fat — it means structuring meals and timing them appropriately.
Natural Approaches for Reflux
1.Supporting Stomach Acid (Where Appropriate)
For people with functional reflux driven by low acid and slow gastric emptying, supporting stomach acid production rather than suppressing it further addresses the root mechanism.
Digestive bitters — herbs including gentian, dandelion, artichoke leaf, and ginger — stimulate the cephalic phase of digestion, increasing gastric acid secretion, bile flow, and enzyme production when taken 10–15 minutes before meals.
Apple cider vinegar in water before meals is a traditional and widely used approach for supporting stomach acid. Its evidence base is largely anecdotal, but clinical experience suggests it is helpful for a subset of people with functional reflux. It is not appropriate where oesophageal damage or active ulcers are present.
Betaine HCl with pepsin is a supplement form of hydrochloric acid used in clinical practice to directly support gastric acid levels. It should be used under guidance — there are contraindications, including concurrent NSAID use and existing ulceration.
Addressing Fermentation and Gas Pressure
If SIBO is driving reflux through gas pressure, treating the bacterial overgrowth is the most direct intervention. A structured herbal antimicrobial protocol, combined with dietary modification and motility support, reduces the fermentative load that is creating the upward pressure.
In the meantime, reducing highly fermentable foods — particularly large amounts of raw vegetables, legumes, wholegrains, and sugars in the evenings when gastric emptying is slower — can reduce symptoms while the underlying issue is being addressed.
Meal Timing and Structure
Not eating for at least 2–3 hours before lying down is one of the most consistently effective reflux interventions. This gives the stomach time to empty before the protective effect of gravity is removed.
Eating in a relaxed, seated position, without rushing, and chewing thoroughly supports the entire digestive cascade from the first moment.
Demulcent Herbs
Herbs that coat and soothe the oesophageal and gastric mucosa can provide symptomatic relief while root causes are addressed. The most useful include:
Slippery elm — contains mucilage that coats the oesophagus and stomach lining, reducing the irritation of acid contact.
Marshmallow root — similar demulcent properties, taken as a cold infusion for maximum mucilage content.
Deglycyrrhizinated liquorice (DGL) — supports the stomach's mucus layer and has anti-inflammatory properties without the blood pressure effects of whole liquorice root.
Diaphragmatic Breathing
The diaphragm shares a structural relationship with the lower oesophageal sphincter. Weak or dysfunctional diaphragmatic breathing — common in people with chronic stress, desk-based work, or a history of disordered breathing — can reduce LOS tone. Structured diaphragmatic breathing practice has evidence for improving reflux symptoms, and is increasingly incorporated into reflux management protocols.
When Reflux Needs Medical Investigation
Not all reflux is functional, and some presentations require conventional investigation before or alongside naturopathic support.
See your doctor if you experience:
Difficulty swallowing, or a feeling of food sticking
Unexplained weight loss
Vomiting blood or passing dark stools
Chest pain (which should always be assessed to rule out cardiac causes)
Reflux that is severe, longstanding, or not responding to any intervention
Barrett's oesophagus — a change in the oesophageal lining associated with chronic acid exposure — requires medical monitoring. If you have had a diagnosis of Barrett's, work with both your gastroenterologist and a naturopath who understands the condition.
The Bigger Picture
Reflux that has been present for years and has been managed with acid suppression is rarely a simple single-cause problem by the time someone seeks a different approach. There are usually multiple contributing factors — low acid, dysbiosis, dietary patterns, stress, and often some degree of oesophageal sensitivity from long-term acid exposure.
The process of resolving it is a structured one: identifying the primary drivers, supporting the gut environment while reducing inflammation, withdrawing acid suppression slowly and under guidance where appropriate, and rebuilding digestive function from the ground up.
It takes time. But it is almost always possible to reach a point where reflux is no longer a daily presence — not managed with medication, but genuinely improved.
Joana Amram is a registered Nutritional Therapist and Naturopath accredited by the ANP (Association of Naturopathic Practitioners) and trained at the College of Naturopathic Medicine in London. She specialises in gut health, IBS, SIBO, microbiome balance, and digestive disorders. Consultations available online worldwide and in-person in Lisbon, Portugal, in English, Portuguese, Spanish, and French.
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Disclaimer: This article is for educational purposes only and does not constitute medical advice. Please consult a qualified healthcare practitioner for personalised recommendations.