Hypochloridia: Why does food sit like a stone

“Why does food sit like a stone in my stomach?” Understanding Low Stomach Acid and Gut Health

If you’ve ever felt like food just sits in your stomach, heavy, bloated, and unmoving, you may have something in common with many of my clients. This sensation, often described to me in clinic as “food sitting like a stone,” may point to a common but under-recognised issue: hypochlorhydria, or low stomach acid.

One of the most common misconceptions I see in clinic is the belief that reflux always means high stomach acid. In reality, low stomach acid is often the culprit. When HCl is insufficient, food sits longer in the stomach, fermenting and creating pressure. This can push contents upward, mimicking acid reflux. Unfortunately, many clients are prescribed PPIs or antacids, which further suppress acid and worsen digestion. Reflux can stem from low acid, not high. PPIs may offer short-term relief but long-term harm. Restoring HCl can reduce reflux, improve nutrient absorption, and rebalance the microbiome.

Hydrochloric acid, or HCl, is a vital component of the highly acid gastric juice. It helps break down protein and supports nutrient absorption, activates digestive enzymes like pepsin, and maintains the stomach’s acidic pH, which protects against the trillions of bacteria entering the gut. When HCl production is compromised, digestion slows, nutrient uptake falters, and microbial imbalances can follow.

Clients with hypochlorhydria often report bloating after meals, painful heartburn or reflux, undigested food in stools, flatulence, halitosis (bad breath), nausea after eating, glossitis (inflammed tongue), and food intolerances or allergies. These symptoms may mimic high stomach acid, leading to misdiagnosis and inappropriate use of antacids or prescribed proton pump inhibitors - (omeprozole, commonly known as Losec, or lansoprazole, and pantoprazole or Famotidine), which all further reduce stomach acid and can worsen the issue.

Symptoms that you might not connect to gut health but commonly evolve over time from insufficient HCl production include nutrient deficiencies, (especially iron, B12, and zinc), microbial overgrowth such as SIBO and parasites, and persistent reflux, bloating, and constipation. 

Several factors can impair HCl production, including long-term use of antacids, medications like Losec, NSAIDs, or antihistamines, Helicobacter pylori infection, chronic stress, ageing, hypothyroidism, diets low in protein or zinc (commonhere in New Zealand), gastric bypass surgery, smoking, alcohol, and high intake of refined carbohydrates.

In clinic, I ask a lot of questions about digestion. Everything from mouth to flush is important to understanding the full digestive journey and uncovering the root cause of symptoms. If we need to explore functional testing  this may include H. pylori screening, iron studies including ferritin and transferrin saturation, albumin and globulin levels, B12 and total protein, gut microbiome analysis for SIBO or parasites, and thyroid panels including TSH, T4, and T3.

I like to pick low hanging fruit as a first priority, so the foundational phase of treatment focuses on gently stimulating and supporting HCl production using targeted herbs and nutrients. It’s the first step in restoring digestive function and comfort after meals. Gentian and ginger are two classic herbal bitters that stimulate the digestive system and I use often to have clients stimulate digestive secretions before meals. Gentian root activates bitter receptors on the tongue and gut lining, enhancing appetite and triggering HCl, preparing the stomach for efficient protein breakdown. Traditionally used in herbal medicine, gentian relieves sluggish digestion and eases bloating and post-meal heaviness. Ginger is one of my favourite warming digestive herbs as it’s so multifunctional. For clients with hypochlorida I use it to activate motility and supports the natural rhythm of the gastrointestinal tract. It promotes gastric emptying, reduces nausea, and the active ingredient gingerols offer anti-inflammatory and antimicrobial properties, making it a valuable herbal medicine in restoring digestive balance.

For clients with confirmed hypochlorhydria or classic symptoms such as indigestion, bloating after protein or undigested food in stool, I typically step it up a notch. Adequate zinc levels are crucial for optimal acid secretion, yet deficiency is common, particularly among vegetarians, individuals with high copper levels such as those using copper IUDs or oral contraception, or those under chronic stress. Zinc carnosine is a clinical favourite for me while we work on your gut health. Zinc carnosine is a poorly absorbed form of zinc, which means it stays at the digestive lining longer and works locally. Which is exactly what I want.. Zinc carnosine also supports mucosal integrity and bolsters immune defences, making it a valuable ally in restoring and protecting gut function.

For some, Betaine hydrochloride is more practical. This is a targeted digestive support that provides supplemental acid to help restore the stomach’s optimal pH. While it doesn’t resolve the underlying cause of low acid, it may offer symptomatic relief and improve protein and nutrient absorption. We’ll use this in cases where herbal medicine isn’t practical, like traveling a lot, or the body is under immense stress, inhibiting the ability to make more HCl. By enhancing gastric acidity, betaine HCl supports iron uptake and helps rebalance the gut microbiome by creating an environment less hospitable to dysbiotic bacteria. There’s a time and a place for this strategy, and herbal bitters. 

Beyond these direct supports, several nutrients are involved in the biochemical pathways that produce stomach acid. Vitamin B2, or riboflavin, is crucial for FAD-dependent enzymes involved in HCl production and supports mucosal healing and energy metabolism.Mineral and electrolyte imbalances may need to be addressed with magnesium, potassium, calcium, zinc, chromium, molybdenum, and selenium to support cellular hydration and acid production.

Supporting HCl production isn’t just about supplements, it’s about rituals, rhythms, and nourishment. Before meals, clients may benefit from squeezing half a lemon or adding a teaspoon of apple cider vinegar into warm water. Herbal teas such as ginger, dandelion, fennel, meadowsweet, chamomile, and lemon balm can gently stimulate digestion. Bitter foods like rocket, cranberry, dill, and grapefruit are also helpful. Slowing down and eating slowly, making sure chewing is sufficient, and digesting in a calm environment plays a big role. Stress management is essential. Mindfulness, yoga, grounding techniques, morning sunlight, and a consistent sleep routine all support parasympathetic activation and digestive readiness. Hydration with mineral-rich water and herbal infusions in a water bottle, can support digestive tone throughout the day. Ginger again comes to mind for the ability to stimulate the migrating motor complex, a key considerations in restoring healthy motility in the gastrointestinal tract. 

If you’ve been living with bloating, reflux, or that heavy “stone-like” feeling after meals, it may be time to explore the root cause, not just mask the symptoms. Low stomach acid, or hypochlorhydria, is often overlooked but plays a central role in nutrient absorption, microbial balance, and digestive comfort. Whether you’re navigating food sensitivities, fatigue, or gut discomfort, restoring HCl production can be a game-changer. In clinic, I work with clients to gently rebuild digestive resilience using targeted herbs, nutrients, and personalised testing. If you’re ready to feel lighter, clearer, and more nourished after meals, reach out—your gut health journey starts with understanding your foundations.