My Thyroid “Aha” Moment: Low Stomach Acid

Thyroid Pharmacist - Dr. Izabella Wentz
In this solo episode, Dr. Izabella Wentz shares the turning point that shifted her Hashimoto’s recovery: discovering that “acid reflux” can stem from low stomach acid (hypochlorhydria) rather than excess stomach acid, as many believe. She explains how hypochlorhydria drives fatigue, brain fog, pain, nutrient deficiencies, SIBO/H. pylori risk, and why supporting digestion can restore energy and clarity fast.
She outlines a practical betaine HCl + pepsin titration, who should avoid it, and simple daily upgrades (like mindful meals, lemon water or diluted ACV, bitters, and thiamine). Real-world response rates and safety notes are included.
What you’ll learn in this episode:
✅Why “acid reflux” can actually mean low stomach acid. In hypothyroidism, stomach acid often runs low, which impairs protein breakdown, fuels overgrowths, increases ammonia (hello brain fog), and leaves you tired after meals. Understanding this flips the usual reflux narrative and opens a path to real relief.
✅How low acid drives fatigue, pain, and mood changes. Poor protein digestion means fewer amino acids for neurotransmitters and repair; when you add in nutrient gaps (B12, iron/ferritin) and inflammatory byproducts, you’ve got a perfect storm for low energy, aches, and low mood.
✅A step-by-step guide to finding your ideal betaine HCl + pepsin dose at meals. Dr. Wentz shares how to determine how many capsules would be most suitable for you, and how to use it safely for best results.
✅When to pause or avoid HCl. It’s not for everyone: if you have active or past peptic ulcers, confirmed H. pylori, current acid overproduction, ingredient sensitivities, or chronic NSAID/steroid use, if you use ongoing PPIs (or you’re weaning), or if you are pregnant/breastfeeding, talk to your clinician first.
✅Simple daily upgrades to raise digestive fire. Eating in a calm state, chewing well, trying diluted lemon water or apple cider vinegar with meals, considering digestive bitters, and assessing thiamine can be surprising helpers for stomach acid and thyroid fatigue.
✅Real-world outcomes and what to expect. In Dr. Wentz’s experience, ~60% of people feel better on HCl, ~33% don’t tolerate it, and ~7% feel no change. Wins often include more energy, less pain/bloating, better mood, smoother bowels, and easier weight balance when digestion finally “clicks.”
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🔗For the full list of resources and products mentioned in this episode, and to get the full episode transcript, see complete show notes here: https://thyroidpharmacist.com/articles/podcast/
Full Transcript
Hashimoto's Healing Breakthrough 0:00
My aha moment with Hashimoto's when I finally got on my healing journey was when i discovered that I actually had low stomach acid despite having acid reflux which conventionally is considered a sign of high stomach Thanks to this aha moment, I was able to have a breakthrough going from sleeping 11 to 12 hours a night to all of a sudden getting seven hours of sleep, waking up bright-eyed and bushy-tailed. My memory started to come back, my brain fog started lift, and my sense of humor came back to what it once was.
And this was after many, many years of fatigue and brain fog. And I'm going to share with you exactly what I did. This was actually one of these steps that encouraged me to keep going, to really encourage me, keep working on my health, and encouraged to get my Hashimoto's into remission. and this is something that's very, very relevant for many people with Hashimoto's, but hardly anybody talks about it, despite the fact that I've put this information out there like 12 years ago. So, welcome to today's episode of Thyroid Pharmacists Healing Conversations podcast.
I'm your host, Dr. Isabella Wentz, your thyroid pharmacist. And as you may know, I am not just a Hashimoto's expert, but I also am somebody who went through my own healing journey with Hashimoto's. chronically exhausted, fatigued, I had brain fog, i had pain in my arms from carpal tunnel, pain all over my body, acid reflux,
What Low Stomach Acid Does 1:35
irritable bowel syndrome, chronic bloating, hair loss, and the symptoms were just like growing with every passing month it seemed. I was actually in my 20s when I diagnosed with Hashimoto's and my symptoms probably started right around when i was 18 during my freshman year in college. So going back to my big aha moment it was figuring out that I had low stomach acid. Now low-stomach acid is something that hardly anybody talks about but when you look at the research the, research actually shows that people with hypothyroidism tend to have low stomach acid or no stomach.
Acid there's some fancy terms for that that I can that, I always tend, to mispronounce but achlorhydria means no, stomach, acid and hypochlorhidria, means low, This really matters because when you have low stomach acid, that means that you do not digest your food properly. That means your foods sits there and becomes food, not for you. You don't get the nutrients out of the food but rather your pathogenic bacteria start to feast on it and overgrow and then this can cause a lot of symptoms. One of things that occurs when you have low stomach acid you can have an increased gut ammonia production.
Ammonia is a neurotoxin so it gives you awful, awful brain fog. You might feel extremely fatigued if you are not properly digesting your food. One of the biggest expenditures our body has is actually digestion. And I know for me, I had noticed that whenever I have a big meal, I would have a lot of fatigue and I also noticed that if I had a meat heavy meal, like a steak, I'd have fatigue. Another thing that I noticed is that when I didn't get enough sleep I sometimes would wake up with diarrhea. It was very much like I felt like my body was broken.
And I didn't really know what to do to fix it. I thought maybe cutting out red meat might be the answer. This seemed to help some of my digestive issues. But you know, I still had the fatigue. It's just like I wasn't having a lot of the diarrhea. So definitely an improvement, but definitely not the root cause. Some of consequences of low stomach acid. Stomach acid is needed for proper protein digestion. So when we eat protein, we break it down into various amino acids, and these amino acid work to repair our body.
They work produce neurotransmitters that make us happy, that help us sleep through the night, help to give us energy throughout the day. When we breakdown our protein we're able to get nutrients out of the protein such as B12, and iron. These are two very very important nutrients for thyroid function, for brain function and for feeling human and not fatigued.
Signs and Consequences of Low Acid 4:46
And then another thing that the stomach acid does is it protects us from pathogens. So let's say we're eating some sushi or another type of food that might have bacteria or parasites. on it. If we have proper stomach acid production we're going to eat that food and the stomach is going kill off all the nasty things and we are not going get sick. In the case that we had low stomach we're gonna eat the same food and there's a chance that that bacteria is going to be able to reproduce in our system, make us sick, or that parasite or other pathogen is gonna get into our systems because it's not been neutralized.
So this is something that I see very commonly happening in people with Hashimoto's. They have this low stomach acid. The additional consequences include having more food sensitivities. When we don't break down our food properly with stomach acids, The food kind of just can become antigenic, which means the immune system starts to recognize it as a foreign invader. The immune systems like, what are these chunks of food doing here? And starts form an attack against the food. Some people might end up with small intestinal bacterial overgrowth.
They might ended up an H. pylori infection. They can become deficient in various nutrients. So I mentioned iron and ferritin, which are very common nutrient deficiencies in Hashimoto's. Also B12, sometimes calcium can also become deficiency. We can also have some overcompensation and some downstream gut effects from not having enough stomach acid. Some of the clues that you might have low stomach acids include having acid reflux or GERD like symptoms, having a low B12 or having low iron or low ferritin on a test, persistent fatigue despite having thyroid meds, I would definitely say if you have hypothyroidism or a history of hypathyroid, there's a really good chance that you do have low stomach acid.
Digestive symptoms such as constipation or diarrhea or feeling like food is just sitting in your stomach and that, you know, get really tired after eating. Sometimes post-nasal drip, this can be also a symptom. Now one of the ways that I found out that i had stomach acid because there isn't really like a test for it that's readily accessible to most people is by doing a trial and error supplement test. So my practitioner at the time suggested that, I tried betaine with pepsin to see if that helped my symptoms and And the thing about betaine with pepsin is you have to kind of titrate the dose because if you get too much of it, it can actually cause a little bit of like symptoms, a bit like acid reflux, um, little of acid burning in your throat.
And so you definitely want to start low and go slow and figure out what your target dose may be.
Betaine HCl Challenge and Dosing 7:56
If you don't take a high enough dose, you're going to find that it doesn't do anything for you. So what I did and what i typically recommend people do is that whenever they're eating a protein containing meal, they start with one capsule of betaine with pepsin and see how they feel. If they fell nothing then at their next protein-containing meal they might take two capsules. If they feel nothing again, they'll increase that to three capsules at their next protein containing meal. And so on and so forth until they fell like a slight burning.
So if you feel a slightly burning at let's say four capsuls, That means that your target dose is actually three capsules. So you want to back off by just one capsule. If you feel that little bit of a burn, that means you got just a little higher dose of stomach acid than you needed. At that point you can drink something like some people would recommend putting a teaspoon of baking soda in a cup and kind of sipping on that. And that generally neutralizes the effect. Although, you know, it does go away within probably a few seconds to a minute for most people.
So you don't necessarily need to worry about that, but then you figured out your target dose. Then your targeted dose would be about three capsules with similar protein containing meals. That can be a really big game changer for your symptoms. I will say I don't recommend going up above like seven or eight capsules per meal unless you're working with a practitioner because sometimes you might you know you may not feel off but there might be something else going on with you like an H. pylori infection if you need that many capsuls.
For most people in my experience the dose is anywhere from two to four capsules per day that they need to really thrive and benefit from. Of the people in my experience that have tried betaine with pepsin, about 60% of them felt better with it. About 33% percent of people felt worse with, and then 7% really saw no change with. Now what are the most common symptoms that improved? One of the biggest symptoms is energy. So for me, I went from chronic fatigue to waking up bright-eyed and bushy-tailed after seven hours of sleep.
I was like, holy cow, like I'm digesting my food, and extracting nutrients from it. This is incredible. Like my brain is coming back on track. The next thing that people report is going to be pain reduction. This wasn't as relevant for me, but for a lot of people with chronic pain, they do find that supporting their digestive stomach acid can relieve that. I was actually quite surprised when I started seeing that with my clients, that it actually makes sense Betaine is actually trimethylglycine, which is something that helps with the inflammatory homocysteine pathway.
So potentially it could also help people with MTHFR gene mutations, as well as those with low stomach acid. A lot of times people reported their mood improved. So they would go from feeling sad and kind of sluggish to feeling happier. For me, like my sense of humor got better. That was like a very subtle shift where I was, oh, okay, I'm back to kind funny and generally I tend to be more funny when I am in a better mood. I wasn't necessarily depressed when started this trial, but I definitely saw a little bit of a shift.
And to me this actually makes sense because there is Part of that pathway that trimethylglycine supports impacts something called SAMe that helps us with our mood and can make us happier. And then also when you break down your proteins, you can create your neurotransmitters. So you create serotonin and your dopamine from your protein and amino acids. When you don't have enough stomach acid on board, then you're not going to be able to make those properly and you might have a deficiency in these.
And then the other thing that a lot of people have found to to helpful would be weight issues. So they were able get to a healthier weight when they where digesting food and that just makes so much more sense because you are no longer going be as inflamed. And then, of course, beyond that, digestive issues. So the bloating was gone, the burping was done, some of the acid reflux symptoms can improve. Some of that constipation, diarrhea, a lot of these things do improve once you support your digestion, which to me is kind of obvious, right?
And some people might have those symptoms.
Who Should Avoid Betaine HCl 12:38
Some people might not have the symptoms, I think some of the less obvious things to me were like, how is it that supporting my digestion helped me recover my energy? How is that some people have such a big reduction in pain and some have dramatic improvements in mood and their weight really improves? So this is something that I find can be very, very helpful for a lot of people with Hashimoto's. Now I will say there are some precautions. times where you should not use this supplement. One time is when you have a history of peptic ulcers because these can actually be made worse by stomach acid.
If you an active H. pylori infection, which can also cause peptal ulcer, then the betaine with pepsin, you know, adding more stomach acids can be a problem as well. If you have an overproduction of acid, which is actually not as common in people with hypothyroidism and in the general population as we've been led to think by pharmaceutical manufacturers, then obviously you would not want to add more acid. People that have sensitivities or allergies to any of the ingredients, potentially pepsin may be pork derived and then there's corn in some formulations.
And then people that are taking acid suppressing medications, such as proton pump inhibitors, you know, if you take this, this is going to kind of like negate its effects. So that's not going do you much good. And you're going be wasting money on both proton, pump, inhibitor. and wasting money on the digestive enzymes. So I generally recommend weaning off of those. And I actually have a protocol that I'm going to link to in the show notes on how you can wean off proton pump inhibitors. It's actually going be a bonus for my new book, Finding and Treating the Root Cause of Irritable Bowel Syndrome.
If you're taking NSAIDs or steroids, these can actually cause you to have more gastric irritation and adding more acid to the bucket can be more problematic. So I definitely don't recommend taking it if you are somebody that takes NSAIDS or Steroids on a regular basis. Of course, if take an ibuprofen here and there like once a month, that's not going to be an issue. I'm talking about people who are chronic daily NSAIDE users and steroid users. So these are things that of course you'd want to discuss with your medical provider and of, course whenever you're pregnant or breastfeeding these, are definitely things you want, to talk with, your health care provider about.
Now there is a risk of you taking too many, you can have some stomach irritation, some of those burning sensations, You're gonna feel that right away and then again I wouldn't go above like seven or eight capsules. in your trial if you're doing this on your own. Most people do need about two to four capsules of betaine and pepsin, and this can vary per brand, but it's been my experience working with a lot of different brands that they tend to kind of try to keep the levels similar.
Ways to Support Stomach Acid 15:44
You know, one of them might have 700 milligrams, another one might 750, Another one may have 600, they're kind all within a similar range. Now, so what do you do if you have low stomach acid, right? So this is a test to see if have it and you can definitely keep taking betaine with pepsin for as long as you need it. Some people do incorporate that into their daily routine and that makes a really, really big difference in their lives. I would consider taking it for maybe one to three months and then at that point things might kind of start to come back on track and you might not need to use it long term, right?
So you just might need a short term support with it. There are things that do cause us to have low stomach acid. One of the biggest things is stress. So if you are stressed out, your stomach is going to be suppressed. And so one of things I really recommend is trying to eat in a mindful state. So you're not standing up running around eating a burger, right? Because that's like how your body picks up stress. You're going to be sitting down and maybe like planning some relaxing music. Think of being at like a nice restaurant, taking some deep breaths and really taking the time to chew your food.
That's going start the digestive process. Having that saliva You know, really chewing your food that's going to kind of kick things off and start kicking in the digestion. The other thing you can do is you take a teaspoon of squeezed lemon juice into a glass of water and sip on that throughout your meals and throughout the day. You can also do this with like a teaspoon of apple cider vinegar. Make sure you dilute it in a glass of water. Do not drink apple-cider vinegar like straight up unless you want to be in pain.
So do not do that. And the other thing that helps a lot of people is thiamine. Thiamin can be helpful for the production of stomach acid. This is another kind of nutrient deficiency that many people with Hashimoto's have. I have written extensively about thiamine. It can be a big game changer for people with thyroid fatigue. Generally speaking, about 600 milligrams per day over the course of three to five days can reverse thyroid fatigue very, very quickly. For some people, they may also benefit from something like digestive bitters.
I like Dr. Shade's Digestive Bitters Formula and the Willena Digestsive biters. i'm going to link to those in the show notes. And, you know, it kind of depends. For Some people they do really well with betaine with pepsin and they take that long term and take it with every meal and it works really, really good for them. Other people might be able to get away with doing some digestive bitters or using some of those, the hot lemon water trick or utilizing thiamine. Some people might need to do all the things to really see a difference.
Generally speaking, a great place to start is going to be doing the Betaine with pepsin challenge. I hope that this can help you feel better. make sure that you remember to take it with your protein containing meals and definitely look into whether you have a thiamine deficiency. I'm going to put a link to my thiaamine article in the show notes and I did an awesome interview with Elliot Overton on different types of thiumine and how they can be of benefit and they how can they be big game changers for Hashimoto's and hypothyroidism.
I would say my you know my top five recommendations for for most people are going to be looking at your stomach acid and supporting that potentially with betaine with pepsin. Sometimes with thiamine that might be a great way to do that. And you have Rootcology. I did add thiamine, benfotiamin, recently to the Rootscologie portfolio. And betaine with pepsin was one of my products that I first came out with because I love it so much, and it's been so helpful and so effective for a lot
Thiamine, Products, and Closing Thoughts 19:48
of people. So if you wanted to try these products, we're going to be offering 10% off for anybody that uses the code podcast. And I have a lot of exciting information to share with you. I Have a brand new book coming out March 17th. It is finding and treating the root cause of irritable bowel syndrome, where we talk about some of these digestive issues and we go really, really deep in them. A lot people with Hashimoto's have digestive issues. Some of them might be diagnosed with irritable bowel syndrome, some of their digestive issue might actually show up as fatigue or brain fog or thyroid antibodies.
Nonetheless, most people with Hashimoto's do really need to work on their gut health. I've outlined the most common and some of the very uncommon reasons why people might have digestive issues, why they might intestinal permeability, how to support all the different pathways of digestion, and how recognize which part of your digestive process might be out of balance and best support yourself through that process. So for those of you watching, this is my new book cover. and I'll be putting some information about it in the show notes.
Right now it's available for pre-order on Amazon and Barnes and Noble and wherever fine books are sold. This is something that I hope will help you on your healing journey. If you are looking for more information on the Betaine with pepsin protocol, I've actually written about in my book Hashimoto's The Root Cause and in a blog on it that I wrote a while ago. So I'm going to link to all of those things in the show notes. I hope this information has been helpful on your healing journey. Honestly, like just supporting your stomach acid can be so so incredibly helpful.
when you have Hashimoto's for your fatigue, for you pain, your mood, and your digestive process. If these are some of the symptoms that are resonating with you, I would highly encourage you to do that stomach acid test. There's a ton of different supplements on the market out there that you can do this with. I love me some high quality companies, Pure Encapsulations, Designs for Health, Zymogen, there's so many wonderful companies out there that make this supplement. And if you wanted to try the Rucology brand, I do have a special offer for you if use the code PODCAST to get some money off of that.
We do a 100% money back guarantee so if your not happy with the product you can return it within 30 days. I know I hope this helps because I know I personally had a supplement graveyard with all of the things that I tried on my healing journey with Hashimoto's and it can be very very it feels very wasteful for one and two you end up trying things and having adverse reactions or they're not You know making you feel better and then you end up spending all of this money and I just don't want that to happen and i've also hand selected products that I know work really really well in my 10 plus years of doing this working with a lot of clients like I Know which stuff is going to work pretty well.
And so I hope that gives you a little bit of ease into trying something for your health. I really appreciate you being here with me, I appreciate your trusting me with your help, and hopefully this has been helpful on your healing journey.
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