Low Stomach Acid: The Overlooked Cause of Reflux, Bloating and Nutrient Deficiencies

20 Jan

When people think of digestive symptoms like reflux, bloating or indigestion, they usually assume they have too much stomach acid.
In clinical practice, the opposite is often true.

Low stomach acid (hypochlorhydria) is one of the most overlooked drivers of digestive dysfunction, and it can quietly affect nutrient absorption, gut health, hormone balance and immune function for years before it’s identified.

What stomach acid actually does

Stomach acid isn’t just there to break down food. Adequate hydrochloric acid (HCl) is essential for:

Proper digestion of protein
Activating digestive enzymes
Absorption of key nutrients such as iron, zinc, B12, calcium and magnesium
Triggering bile release from the liver and gallbladder
Protecting against bacteria, parasites and pathogens entering the gut

When stomach acid is low, digestion becomes inefficient very early in the digestive process, and downstream symptoms often follow.

Symptoms of low stomach acid

Low stomach acid can look surprisingly similar to high acid, which is why it’s often mismanaged. Common signs include:

Reflux or heartburn, especially after protein-rich meals
Bloating shortly after eating
Feeling overly full from small meals
Belching, nausea or food sitting “heavy”
Undigested food in stools
Iron deficiency or low B12 despite adequate intake
Recurrent gut infections or dysbiosis

Suppressing acid with medications may reduce symptoms temporarily, but it does not address the underlying issue and can worsen nutrient depletion over time.

Why reflux can occur with low acid

Reflux is not always caused by excess acid. In many cases, it’s related to poor stomach emptying and pressure.

When stomach acid is insufficient:

Protein is not broken down properly
Food remains in the stomach longer
Fermentation increases
Pressure builds, pushing contents upward

This can irritate the oesophagus even when acid levels are low.

What causes low stomach acid?

Low stomach acid can develop due to several factors, including:

Chronic stress and sympathetic nervous system dominance.
This shuts off ‘rest and digest’ mode required to allow digestive secretions to be released.
Long-term use of antacids or proton pump inhibitors
Eating quickly or while stressed
Zinc deficiency
Ageing (though this can occur at any age)
Chronic infections such as H. pylori

It is very common in people with long-standing digestive symptoms, hormonal imbalances and fatigue.

Why low stomach acid affects hormones and energy

Without adequate stomach acid:

Iron and B12 absorption declines, which can impact energy and thyroid function
Protein digestion suffers, affecting neurotransmitters and hormones
Bile release is impaired, reducing fat digestion and estrogen clearance

This is why digestive issues often sit underneath hormone symptoms, even when hormones appear “normal” on blood tests.

The takeaway

Reflux and bloating are not always about excess acid. In many cases, they are signs of impaired digestion upstream.

Addressing low stomach acid is about restoring digestive signalling, nervous system balance and nutrient status, not suppressing symptoms.

jess taylor