The Heartburn Myth: Too Much Stomach Acid — or Too Little?

Here's a story I've heard a hundred times. Someone gets heartburn. They go to the doctor. They're told they have too much stomach acid, handed a little purple pill, and sent home. The burning calms down for a while — so the pill must be working, right? But months later they're still on it. Then years. The acid reducer that was supposed to be a short fix has quietly become a permanent prescription, and the underlying problem never actually got fixed.

I think that whole story is backwards. And once you understand what stomach acid is actually for, you can't unsee it.

What stomach acid is actually for?

Stomach acid gets treated like a villain. It's not. It's one of the most important tools your body has, and you're supposed to have a lot of it.

Strong stomach acid does at least four jobs you can't live well without:

- It kicks off protein digestion by switching on the enzyme pepsin. - It unlocks minerals — iron, calcium, magnesium, zinc — so your gut can actually absorb them. - It frees up vitamin B12 that's bound to the protein in your food, so it can be absorbed further down. - It acts as a gatekeeper, killing most of the bacteria and parasites that ride in on your food before they can set up shop.

In other words, acid isn't the enemy of digestion — it's where good digestion begins (I walk through the whole chain in "Digestion" post). So the idea that the cure for indigestion is to get rid of your acid should at least make you raise an eyebrow.

The part most people never hear: low acid can cause reflux too

Now, I want to be straight with you, because honesty is the whole point of this site. The mainstream explanation is that reflux happens when the valve at the top of your stomach (the lower esophageal sphincter) gets lax and lets acid splash up into your esophagus. That's real, and for some people it's the main story.

But there's a second model — championed by Dr. Jonathan Wright in his book Why Stomach Acid Is Good for You — that I think deserves a seat at the table. It's a hypothesis, not settled textbook science, so I'll call it that. But it explains a lot of cases the standard story doesn't, and it goes like this:

When you don't make enough acid (a condition called hypochlorhydria, which becomes more common as we age), your stomach has a hard time doing its job. The valve at the bottom of your stomach — the pyloric sphincter — is partly triggered to open by acidity. Without enough acid, the meal sits there too long. Food that lingers in a warm, low-acid stomach does what food always does in those conditions: it ferments. Fermentation makes gas. Gas builds pressure. And that pressure can push the small amount of acid you do have up through the top valve and into your esophagus — where it burns.

If that's what's really happening, then handing someone an acid reducer is like trying to fix a car that won't start by disconnecting the battery warning light. You've muted the alarm. You haven't fixed the engine. In fact, you may have made the root problem — too little acid — even worse.

What acid reducers actually do

Proton pump inhibitors (PPIs) — omeprazole, esomeprazole, and the rest — are very good at one thing: shutting down acid production. They work. They genuinely heal acid-damaged esophagus tissue, and for short-term use or true high-acid conditions, they have a place.

My problem is with handing them out as a permanent fix to millions of people, often without ever checking whether the person had too much acid or too little in the first place. Because when you suppress acid for years, you start paying for all four of those jobs acid was doing:

- B12 runs low - Here's the precise mechanism, because the common explanation gets it wrong: PPIs don't block intrinsic factor. They reduce the acid that frees B12 from your food in the first place, so less of it ever becomes available to absorb. Long-term users show more B12 deficiency in large studies (Lam, JAMA 2013).

- Magnesium can drop - The FDA issued a safety communication back in March 2011 warning that long-term PPI use (usually over a year) can cause low magnesium and magnesium runs hundreds of reactions in your body (see the hypomagnesaemia review below).

- The gatekeeper goes offline - With the acid barrier suppressed, bacteria colonize where they shouldn't. In observational studies, long-term PPI use is associated with small-intestinal bacterial overgrowth, a less diverse gut microbiome, and a roughly 1.7–1.8× higher rate of C. difficile infection (Imhann, Gut 2016; AGA review, Gastroenterology 2017). On H. pylori specifically, it's a two-way street — low acid makes the stomach easier to colonize, and an established infection itself lowers acid — so I won't oversell it, but the direction is not reassuring.

- There are associations worth knowing about - Long-term PPI use has been associated with higher rates of bone fracture and chronic kidney disease in observational studies. I'll be honest with you the way I always try to be: these are associations, not proven cause-and-effect, and the dementia scare you may have read about hasn't held up. But "we're not 100% sure it causes harm" is a strange reason to stay on a drug for a decade for a problem it was never fixing.

What I'd look at instead

I can't diagnose you, and nothing here is a reason to stop a medication on your own (more on that in a second). But if I were trying to get to the root instead of muting the alarm, this is the territory I'd explore, usually with a knowledgeable practitioner:

- Eat real food and slow down - Chew thoroughly. Stop eating in a rush and standing up. Big, fast, processed meals are reflux fuel. - Don't drown your meals - Pounding a lot of fluid with food can dilute the acid you need to do the job. - Build the meal around nourishing animal foods - They're the densest sources of the very things low acid robs you of B12, iron, zinc, and quality protein. - Mind the timing - Lying down or going to bed on a full stomach invites reflux. Give yourself a few hours. - Consider herbal bitters before a meal - This is one of my favorites because it's gentle, traditional, and it works with your body instead of shutting it down. Bitter herbs like gentian, dandelion, and ginger have been used for centuries to wake up digestion. The mechanism is real. Tasting bitter on your tongue signals your stomach to make more of its own acid and your whole digestive tract to get ready for food. A few drops or a splash in a little water 10–15 minutes before eating is a time-honored way to support digestion from the top. One honest caveat that fits the theme of this whole post: because bitters increase your acid and digestive activity, they tend to help the low-acid picture but can aggravate the other kind of reflux (the lax-valve, genuinely-too-much-acid kind). So start low, pay attention, and back off if they make you feel worse. Your body will tell you which camp you're in.

- Consider that you might need more acid, not less - Beyond bitters, some people work with a practitioner on stronger digestive supports like betaine HCl, not to "treat reflux," but to help the stomach do its job. This is exactly the kind of thing to do with guidance. Betaine HCl should be avoided by anyone with an active or suspected ulcer, anyone taking NSAIDs or corticosteroids, and anyone already on acid-reducing medication. - Rule out H. pylori properly rather than guessing.

This is root-cause work, and it's the same philosophy behind everything I teach in the foundations of health article. Give the body what it needs, remove what's in the way, and let it do what it was built to do.

One important safety note

Please do not read this and stop your acid reducer cold turkey. There's a well-documented effect called rebound acid hypersecretion. When you suddenly stop a PPI, your stomach can come roaring back with more acid than before, and you'll feel worse — which is exactly how people get convinced they "need" the drug for life. A controlled study even produced brand-new reflux symptoms in healthy volunteers just by putting them on a PPI and then stopping it (Reimer, Gastroenterology 2009). If you and your doctor decide to come off one, it's done gradually, on purpose, while you address the root cause underneath. That's informed, careful, adult medicine — and it's your choice to make.

So how do you actually get off them?

There's a real, structured way to come off acid reducers. The approach taught by the Nutritional Therapy Association and Dr. Jonathan Wright and the single most important rule is this: don't improvise it alone, and if you're on a prescription acid reducer, talk to your prescribing doctor before you change anything. Over-the-counter PPIs are more forgiving, but even then most people are far more comfortable easing off than quitting overnight — because of that rebound effect.

Here is an overview of the gradual process:

- You taper, you don't slam the brakes - A typical wean steps the dose down (for example, every other day) over roughly 4–8 weeks, at a pace your symptoms allow.

- You soothe the stomach while it re-calibrates - Gut-healing foods and nutrients like bone broth, DGL licorice, aloe, slippery elm, marshmallow root, cabbage juice. Calming the lining during the transition.

- You rebuild your own acid - As you come off, you gently add acid support from a little raw apple cider vinegar in water before meals, and HCl/enzyme support with meals. So your stomach can take its job back. (Same caution as before: HCl isn't for anyone with an ulcer, on NSAIDs or steroids, or still on acid-reducing medication (This is a with-a-practitioner step.)

- You have tools for the rough moments, - which your practitioner walks you through.

- You dial in your dose - Toward the end, a simple "HCl Challenge" finds how much acid support you actually need — because you're bio-individual.

Because this matters so much, I put the whole thing into a free, plain-English companion: a step-by-step guide to weaning off acid reducers. It walks through exactly how a careful, gradual wean works so you can do it the right way — at your own pace and, especially for any prescription medication, in coordination with your doctor. Don't go it alone, and never change a prescribed medication without your prescribing physician.

The bottom line

For a lot of people, the heartburn story has it exactly upside down. The problem may not be too much acid — it may be too little, and a stomach that can't finish the job. Suppressing that acid for years can quiet the burn while slowly costing you nutrients and gut defenses you can't afford to lose.

But here's the hopeful part, and I mean this: your stomach almost certainly isn't broken. It's been muffled. When you slow down, eat real food, and gently help it make its own acid again — with simple things like herbal bitters before a meal — the body tends to do exactly what it was built to do. The goal was never a lifetime prescription. The goal is a stomach that works again — and for most people, that's well within reach.

Sources

1. Wright JV, Lenard L. "Why Stomach Acid Is Good for You: Natural Relief from Heartburn, Indigestion, Reflux and GERD." M. Evans, 2001.

2. Fasano A. "All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability." F1000Research 2020;9:69.

3. Vaezi MF, Yang Y-X, Howden CW. "Complications of Proton Pump Inhibitor Therapy." Gastroenterology 2017;153(1):35–48.

4. Lam JR, Schneider JL, Zhao W, Corley DA. "Proton Pump Inhibitor and H2-Receptor Antagonist Use and Vitamin B12 Deficiency." JAMA 2013;310(22):2435–2442.

5. Reimer C, et al. "Proton-Pump Inhibitor Therapy Induces Acid-Related Symptoms in Healthy Volunteers After Withdrawal of Therapy." Gastroenterology 2009;137(1):80–87.

6. Imhann F, et al. "Proton pump inhibitors affect the gut microbiome." Gut 2016;65(5):740–748.

7. Hypomagnesaemia associated with long-term use of proton pump inhibitors (review). PMC 2015. (See also FDA Drug Safety Communication, March 2011, on low magnesium with long-term PPI use.)