If you’ve been told that you have IBS, you’ve probably tried FODMAP, eliminated various foods, and perhaps learned to live with a stomach that never feels quite right. But there is a cause behind the symptoms, and sometimes it is completely different from what you first think.
IBS is one of our most common digestive diagnoses. But it is also a diagnosis based on symptoms, and does not say anything about the cause of why you actually have these problems.
In other words, five different people with an IBS diagnosis may have five completely different reasons why their stomach is causing problems.
One of these causes, which is often overlooked, may be low stomach acid. Since stomach acid is the very first step in the digestive process, problems there can create symptoms further down the gastrointestinal tract.
Stomach acid is the first step in digestion
The role of stomach acid is much greater than simply creating the right pH level in the stomach. It also helps break down protein in particular, activates the digestive enzyme pepsin, and signals to the rest of the digestive system that it is time to take over.
Stomach acid also functions as the body’s first checkpoint, preventing bacteria and microorganisms that we may have ingested with our food from continuing into the small intestine.
When food is not broken down properly
If stomach acid is low, food is not broken down as effectively as it should be. At the same time, the stomach’s checkpoint is also affected and cannot do its job as well. This allows both more undigested food and more bacteria to pass further down the digestive system.
This gives the bacteria further down in the intestine more to work with. When they begin breaking down the food, gases are produced that can cause bloating, a feeling of pressure, and stomach cramps—symptoms that many people immediately associate with IBS.
In integrative and functional medicine, it is often said that people with low stomach acid experience the greatest discomfort after meals high in protein. This may be because hydrochloric acid is needed to activate the enzyme pepsin, which is the enzyme that initiates protein breakdown.
However, there are still few clinical studies that have specifically investigated the connection between low stomach acid and particularly pronounced symptoms after protein-rich meals.
The problems can continue further down in the intestines
Low stomach acid has also been linked to an increased risk of small intestinal bacterial overgrowth, SIBO. One possible explanation is that more bacteria survive the journey through the stomach when the environment there is not acidic enough to kill them. At the same time, the bacteria further down in the intestines receive more nutrients from food that has not been broken down as effectively.
SIBO can in turn cause symptoms similar to those of IBS: gas, bloating, abdominal pain, and diarrhea, constipation, or alternating bowel movements.
This does not necessarily mean that low stomach acid causes IBS or that everyone with IBS also has SIBO. But because the symptoms are often so similar, it is not always obvious what is actually behind the discomfort.
How does low stomach acid differ from IBS?
Unfortunately, it is not possible to determine the underlying cause of your symptoms based on symptoms alone. But certain patterns may offer clues.
Symptoms that may occur with both IBS and low stomach acid:
- Bloating
- Gas
- Burping
- Stomach cramps or discomfort after eating
Symptoms often associated with low stomach acid in integrative and functional medicine:
- Discomfort, especially after meals high in protein
- The feeling that food remains in the stomach for a long time
- Early satiety
- Frequent burping immediately after eating
These symptoms are primarily based on clinical observations and are biologically plausible given the function of stomach acid. However, it is worth noting that research has not yet progressed as far as the clinical observations.
Symptoms more often associated with IBS:
- Recurring abdominal pain associated with bowel movements
- Diarrhea, constipation, or alternating bowel movements
- Discomfort that recurs over a longer period of time
Would you like to support your digestion?
If you recognize yourself in what we have described, there are dietary supplements that many people use to support digestion. In integrative and functional medicine, bitters, digestive enzymes, and betaine HCl are some of the most common options.
They are not suitable for everyone and do not replace the need to understand what is actually behind the discomfort, but they may be a helpful form of support along the way.

