Why You Actually Need Stomach Acid: The Hidden Risks of Acid Suppression

For years, stomach acid has been villainized. We’re conditioned to reach for antacids or proton pump inhibitors (PPIs) like omeprazole at the first sign of heartburn. But what if the real problem isn’t too much stomach acid—but too little?

Despite conventional thinking, stomach acid is not just safe—it’s essential. It plays a critical role in digestion, nutrient absorption, immune defense, and even gut microbiome balance. Chronic suppression of stomach acid, particularly through long-term use of PPIs, can result in a cascade of negative health effects that impact nearly every system in the body.

In this article, we’ll explore why stomach acid is so vital, what happens when you don’t have enough, and the surprising dangers of suppressing it for the long haul. We’ll also build on insights from our detailed post on proton pump inhibitors and nitric oxide/cardiovascular risk.

What Is Stomach Acid, Really?

Stomach acid, also known as hydrochloric acid (HCl), is secreted by parietal cells in the lining of your stomach. It maintains a highly acidic pH (typically between 1.5 and 3.0), which is necessary for:

• Breaking down protein into absorbable amino acids

• Activating digestive enzymes like pepsin

• Absorbing key micronutrients (iron, calcium, magnesium, B12, zinc)

• Killing harmful bacteria, parasites, and viruses

• Signaling downstream digestive processes in the pancreas and gallbladder

In other words, stomach acid is the chemical cornerstone of digestion and gut health.

The Myth of “Too Much Acid”

Many people blame heartburn and reflux on excess acid, but in many cases, it’s the opposite: they may not have enough stomach acid.

When acid production is low (a condition called hypochlorhydria), food sits in the stomach longer than it should. This can lead to pressure buildup, fermentation, and backflow into the esophagus—the root cause of what feels like “acid reflux.” Suppressing acid further may reduce symptoms temporarily but fails to resolve the underlying issue.

The Digestive Domino Effect of Low Stomach Acid

1. Impaired Protein Digestion

Protein digestion begins in the stomach. Low stomach acid reduces the activation of pepsin, the enzyme that breaks down proteins. Undigested proteins can trigger food sensitivities, irritate the gut lining, and contribute to inflammation.

2. Poor Nutrient Absorption

Several nutrients require an acidic environment to be properly absorbed:

• Vitamin B12: Requires stomach acid to release it from protein-bound food sources and to support intrinsic factor, a protein that helps it absorb in the small intestine.

• Iron: Acid converts dietary iron into a form that can be absorbed in the small intestine.

• Magnesium & Calcium: Acid is required for optimal solubility and absorption.

• Zinc: Essential for immune function and wound healing, zinc absorption is impaired in low-acid environments.

Over time, low acid can lead to chronic nutrient deficiencies with wide-reaching health consequences.

3. Bacterial Overgrowth and Dysbiosis

Your stomach’s acidity is a defense system. It kills pathogens and prevents harmful bacteria from colonizing the upper GI tract. When stomach acid is low, it creates an open invitation for bacteria to thrive, leading to:

• Small Intestinal Bacterial Overgrowth (SIBO)

• H. pylori infection

• Yeast overgrowth

• Chronic bloating and gas

These conditions further compromise digestion and may perpetuate inflammation.

4. Increased Food Allergies and Autoimmunity

Poorly digested proteins are more likely to trigger immune responses. This can increase the risk of developing food allergies or sensitivities. Chronic exposure to these partially digested food antigens may drive systemic inflammation and contribute to autoimmune conditions like Hashimoto's thyroiditis, rheumatoid arthritis, and celiac disease.

Low stomach acid is also linked to increased intestinal permeability ("leaky gut"), another major contributor to immune dysregulation.

5. Constipation, Diarrhea, and GI Dysfunction

Incomplete digestion in the stomach affects the entire GI tract. Without proper acid signaling, the pancreas and gallbladder don't release sufficient enzymes and bile. This leads to poorly digested fats and carbohydrates in the intestines, causing:

• Constipation

• Diarrhea

• Undigested food in stools

• Gut motility issues

Risk Factors for Low Stomach Acid

Several lifestyle and medical factors can suppress stomach acid production:

• Chronic stress

• Long-term PPI or antacid use

• Aging

• H. pylori infection

• Gastric bypass or stomach surgeries

• Overeating or frequent snacking

• Poor chewing habits

These risk factors compound over time, often going unnoticed until symptoms appear.

PPIs: Necessary at Times, But Risky Long-Term

As discussed in our in-depth blog on PPIs and cardiovascular health, proton pump inhibitors suppress stomach acid to reduce symptoms of GERD, ulcers, or gastritis. However, long-term use is associated with:

• Suppression of nitric oxide production (linked to higher blood pressure and cardiovascular disease)

• Disrupted lysosomal activity (damaging cellular waste clearance)

• Increased risk of infections like C. difficile

• Bone loss and fractures

• Impaired B12, magnesium, and iron absorption

Even short-term use should include a strategy to address underlying causes and eventual discontinuation.

How to Know if You Have Low Stomach Acid

Common signs include:

• Bloating, gas, or heaviness after meals

• Belching

• Undigested food in stool

• Food sensitivities

• Nutrient deficiencies (especially B12, iron, magnesium)

• Heartburn that improves with acid support

• Weak or cracked fingernails

A practitioner can assess your acid levels using the Heidelberg test, Betaine HCl challenge, or clinical symptoms.

How to Support Stomach Acid Naturally

1. Chew Thoroughly

Digestion starts in the mouth. Chewing stimulates stomach acid and prepares food for proper breakdown.

2. Stop Eating on the Run

Stress inhibits stomach acid production. Create a calm, seated mealtime environment to support parasympathetic nervous system activation.

3. Incorporate Apple Cider Vinegar or Lemon Water

A tablespoon of apple cider vinegar or a squeeze of lemon juice before meals may help prime digestion.

4. Use Digestive Bitters

Herbal bitters can stimulate gastric secretions and promote bile flow.

5. Betaine HCl With Pepsin (pH+)

Supplemental HCl can help restore acidity. Use only under practitioner supervision, especially if ulcers or active gastritis are suspected.

6. Avoid Overeating and Late Meals

Give your body time to digest and rest. Overeating dilutes stomach acid and stresses the system.

7. Correct Micronutrient Deficiencies

Replenishing nutrients like zinc and magnesium can help restore parietal cell function and acid production.

Identifying and Treating the Root Cause of Reflux

Rather than suppressing symptoms with PPIs, functional medicine takes a deeper look at why reflux or GI symptoms occur in the first place. Common contributors include:

• Food sensitivities (gluten, dairy, soy)

• Gut dysbiosis

• H. pylori infection

• Stress and poor vagal tone

• Structural issues like hiatal hernia

By addressing the root cause, long-term healing becomes possible without lifelong acid suppression.

When Acid Support is Better Than Suppression

If low acid is the problem, the right approach isn’t to suppress more — it’s to restore function. That might mean:

• Betaine HCl supplementation (pH+)

• Digestive enzyme support

• Lifestyle modifications

• Treating bacterial overgrowth or infections

This root-cause strategy can resolve reflux, improve digestion, and prevent complications associated with acid suppression.

Final Thoughts

Stomach acid is not your enemy. It’s a vital, often misunderstood component of healthy digestion and immune protection. While PPIs can offer short-term relief for specific conditions, long-term acid suppression can cause far more harm than good.

If you’re struggling with chronic reflux, indigestion, or digestive dysfunction, don’t settle for symptom suppression. Look deeper, ask better questions, and work with a practitioner who can help restore proper digestive function from the inside out.

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References

1. Martinsen TC, Bergh K, Waldum HL. Gastric juice: a barrier against infectious diseases. Basic Clin Pharmacol Toxicol. 2005.

2. Heidelbaugh JJ. Proton pump inhibitors and risk of vitamin and mineral deficiency. Ther Adv Drug Saf. 2013.

3. Ghebremariam YT, et al. Proton pump inhibitors and vascular function. Am J Physiol Heart Circ Physiol. 2016.

4. Takahashi Y, et al. Proton pump inhibitors inhibit lysosomal acidification and autophagic flux. J Gastroenterol. 2020.

5. Reimer C. Safety of proton pump inhibitors. Best Pract Res Clin Gastroenterol. 2013.

6. Williams C, McColl KE. Review article: proton pump inhibitors and bacterial overgrowth. Aliment Pharmacol Ther. 2006.