Low Stomach Acid: The Root Cause of Acid Reflux & Candida
You’ve been told acid reflux is caused by too much stomach acid.
WRONG. 😤
That idea has been fed to you by a multi-billion-dollar industry that profits off suppressing your symptoms — but it doesn’t actually solve the problem.
In functional medicine, we see the truth: most people with acid reflux actually have low stomach acid. And the fix isn’t another supplement or antacid.
Let’s dive into the real root causes your doctor never told you about, how to test for them, and what to do instead.
What Is Low Stomach Acid (Hypochlorhydria)?
Low stomach acid, or hypochlorhydria, is when your body doesn’t produce enough hydrochloric acid (HCl) to properly digest food.
You need stomach acid to:
- Break down protein
- Absorb nutrients like zinc and B12
- Kill off bad bacteria, viruses, and parasites
Without enough acid, your digestion slows down. Undigested food ferments in your gut, feeding pathogens like Candida and SIBO.
And here’s the kicker: low stomach acid can cause symptoms that look like “too much” acid.
Low Stomach Acid Symptoms
If you have ANY of these symptoms, low stomach acid might be the real issue:
- Acid reflux or heartburn (yep — that’s right 👀)
- Bloating after meals
- Constipation
- Undigested food in your stool
- Candida overgrowth
- Food sensitivities
- Nutrient deficiencies (especially zinc)
- Belching or burping
- Feeling heavy after eating
Still not sure? Keep reading. We’ll show you how to test for it at home.
Root Causes of Low Stomach Acid: It’s Not Just Aging
Spoiler: low stomach acid doesn’t just happen.
There are 3 MAIN root causes I see in my practice:
1. H. Pylori Overgrowth (The Hidden Parasite in Your Stomach)
H. pylori is a sneaky little pathogen that lives in the stomach. It’s one of the most common infections I find in clients with acid reflux.
And it’s almost always missed by standard testing.
This bacteria suppresses your stomach acid — so if you’ve got H. pylori, taking antacids or drinking lemon water won’t fix the problem.
👉 Want to test for it? I use the GI-MAP test to detect H. pylori accurately (hospital tests often miss it).
2. Zinc Deficiency (The Acid Blocker Nobody Talks About)
You NEED zinc to make stomach acid. But if you’re deficient, your gut will stay in low gear.
The problem? You can become zinc deficient because of...
- PPI (acid blocker) use
- Low stomach acid itself (zinc needs acid to be absorbed)
- Copper toxicity (more on that next)
👉 You can check your zinc status on a regular CMP panel by looking at your Alkaline Phosphatase (ALP). If it’s <70? That’s a red flag.
3. Hidden Copper Toxicity (The Root of the Root)
Copper and zinc balance each other. When copper is too high (from birth control, IUDs, or stress), it pushes zinc down.
This imbalance leads to:
- Hormone problems (PMS, infertility, PMDD)
- Emotional instability
- Skin issues
- Zinc deficiency (which lowers stomach acid)
📌 I test copper + zinc with an HTMA test — no blood draw needed.
Why Antacids, Lemon Water, and Apple Cider Vinegar Don’t Fix the Problem
So you’ve got reflux. You try antacids. Then lemon water. Then ACV.
For a second, you feel better. But the relief is short-lived.
Here’s why:
- Antacids suppress stomach acid even more
- Lemon and ACV only temporarily boost acid — they don’t fix the why
- H. pylori LOVES acid. If you add more acid before treating the infection? You feel WORSE.
Treating symptoms without the full picture is like putting a Band-Aid on a bullet wound.
You don’t need more band-aids. You need a roadmap.
How to Actually Fix Low Stomach Acid (Without Guesswork)
Here’s the roadmap we use inside the Better Belly Blueprint — and how I’ve helped hundreds of women fix their reflux, constipation, and bloating for GOOD:
Step 1: Test for Root Causes
We don’t guess — we test. The 2 labs we use?
- GI-MAP (for H. pylori + pathogens)
- HTMA (for copper/zinc balance)
Want to DIY test stomach acid at home? Try the baking soda burp test (free in our constipation guide at betterbellytherapies.com/constipation).
Step 2: Build Vitality First
Before jumping into kill protocols or supplements, we build the body up first:
- Liver support
- Drainage pathways
- Nervous system regulation
This makes every protocol after it work better. Way better.
Step 3: Remove Infections (Like H. Pylori)
Once your body's ready, we go after the root bugs — starting with H. pylori. Kill that, and your stomach acid can rise again.
Step 4: Replenish Zinc
Zinc is your stomach acid’s best friend. We use bioavailable zinc (not the cheap stuff) to restore your natural digestive fire.
Step 5: Wean Off PPIs (Safely)
This step is LAST — because if you skip ahead, you’ll crash. You must treat the root first.
Want our protocol? Listen to Podcast Episode 287 on safely weaning off PPIs.
Quick Recap
Low stomach acid isn’t random — it’s reversible when you:
- ✅ Test for H. pylori and zinc/copper balance
- ✅ Build vitality before killing bugs
- ✅ Treat pathogens like H. pylori
- ✅ Replenish zinc stores
- ✅ Wean off acid blockers after the body is ready
FAQs
Can low stomach acid cause reflux?
Yes — it's one of the most common causes of acid reflux, despite what conventional medicine says.
What’s the best test for low stomach acid?
We recommend the baking soda test (for DIY) or checking zinc via HTMA and ALP levels.
Should I take apple cider vinegar for digestion?
Maybe — but only short-term. If you have H. pylori, it could backfire. Test first.
How can I fix my stomach acid naturally?
Find and treat the root cause: H. pylori, zinc deficiency, or copper toxicity.
Is acid reflux medication bad?
It’s not evil — but it can worsen long-term gut health by lowering your natural acid.
Want Step-by-Step Help? 🎯
If you’re tired of wasting money on supplements that don’t work...
If you’ve seen every specialist and STILL have bloating, reflux, or constipation...
We’ve got a roadmap.
👉 Apply for the Better Belly Blueprint and get access to personalized testing, expert protocols, and step-by-step coaching.
You don’t need to stay stuck. You need the right help.
Written by Allison Jordan, FDN-P — gut health specialist and founder of Better Belly Therapies.
EPISODES MENTIONED:
- 233// H. Pylori: Symptoms of H. Pylori, How to Interpret H. Pylori Test Results, and Why H. Pylori Treatments Fail
- 159// Copper Toxicity: A Hidden Cause Behind Constipation & PMS
- 287// How to safely get off PPI’s and reverse acid reflux naturally
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