The 4 Best Digestive Health Supplements, According to a Nutritionist

If you suffer from digestive woes, it can profoundly affect your quality of life. Both Stacy and I know personally how uncomfortable GI symptoms can be.  Between the two of us we’ve struggled with IBS, SIBO, GERD, and LPR, which means we have dealt with our share of gas, bloating, constipation, diarrhea, abdominal pain, acid reflux and silent reflux.  Yikes! 

We are happy to report that our guts are in a much happier place thanks to dietary changes, stress management and some choice supplements.  This article will reveal the best digestive health supplements to help ditch those uncomfortable symptoms.

Will a supplement make it all go away?  If you’re looking for a quick fix, you’re in the wrong place. Believe us, we wish it was that easy.  The best supplements for digestive problems won’t work very well unless you are also following best practices for gut health. This can mean any or all of the below:

Yes, achieving optimal gut health is a project, but it is possible! To tackle it head on, it requires treatment from all angles – diet, lifestyle, exercise, and supplements for digestion.

The best digestive supplement for you will vary depending on your symptoms and whether you have any nutrient deficiencies.

How to Choose a Digestive Health Supplement

Before you decide on the best digestive supplement to take, you should first ask yourself the following questions:

What is your diet like? Could it be lacking in anything and do you have any nutrition deficiencies? Top nutrient deficiencies and insufficiencies we see in our practice that can affect gut health include:

  • Vitamin B12 – A deficiency has been shown to alter the gut microbiome (the collection of good gut bacteria that majorly influences digestion) in a negative way, leading to impaired gut health(1). Vitamin B12 deficiency can also lead to diarrhea and vomiting.
  • Iron – Iron deficiency can cause the microbiome to become unbalanced, which can cause digestive symptoms(2).
  • Zinc – Zinc plays a huge role in gut health, and helps maintain the  integrity of the intestinal barrier to prevent leaky gut. We also need an adequate supply of zinc to produce stomach acid(3).
  • Vitamin D – Reduces inflammation in the gut and helps fortify the intestinal barrier to keep harmful bacteria out(4). An inflamed intestinal barrier can lead to food sensitivities and more GI symptoms.

Ask your doctor to test these at your next visit to know your levels. It’s virtually impossible to heal your gut without the right nutrition building blocks for repair.

What symptoms are you experiencing? The best digestive health supplement to take will depend on your primary symptoms – whether that be constipation, diarrhea, bloating, or acid reflux.

Are you addressing your symptoms in other ways? Diet, physical activity, stress, and sleep all impact digestive symptoms. These areas should all be addressed for maximum benefits from a supplement.

With that said, once you have addressed the nutrient deficiencies you may want to consider four of the best digestive health supplements we use in our practice, based on scientific evidence.

1.   Probiotics for Diarrhea

When it comes to the best supplements for digestion, especially diarrhea, probiotics are high on the list. Probiotics are beneficial bacteria that can support healthy digestion.

There are hundreds of probiotics for digestion on the market to choose from, depending on your symptoms and goals.

How it works:

Probiotics prevent the build-up of bad bacteria in your gut that can cause unpleasant symptoms. They act in the body in various ways, such as (5):

  • Keeping bad gut bacteria from getting out of control
  • Preventing bad bacteria from your diet from entering your bloodstream, which can lead to symptoms across the body.  Think rashes, joint pain, brain fog and more.
  • Breaking down and absorbing nutrients and medications

It’s best to choose a specific probiotic strain based on your primary symptom.

For diarrhea, we would recommend the strain Saccharomyces boulardii. S. boulardi has also been shown to help specifically eradicate SIBO and H. pylori, a common bacterial infection in the stomach(6).

You may also benefit from the probiotics that are found in fermented foods in lesser amounts such as yogurt, kefir, kimchi, sauerkraut, and kombucha.  When it comes to fermented foods, we always recommend starting with a small amount and gradually increasing your serving size.  Too many fermented foods can cause gas, especially if you aren’t used to eating them. I learned this the hard way when I tried kombucha for the first time before a massage at a spa… I was beyond bloated and gassy.  It totally ruined my relaxing, self-care moment.


Do not take probiotics if you have a suppressed immune system. Minor gastrointestinal side effects in the first few weeks of use are rare but possible(7).

Always speak to your medical doctor prior to taking any new supplement.

2.   Partially Hydrolyzed Guar Gum for Diarrhea, Constipation & SIBO

Partially hydrolyzed guar gum (PHGG) is a type of prebiotic fiber.  Prebiotics are often confused with probiotics. Prebiotics are healthy fibers essential for gut health and can help with a multitude of symptoms such as diarrhea and constipation.  This particular type of fiber has also been shown to help eradicate SIBO when taken in conjunction with antibiotic or herbal antimicrobial treatment(8).

How it works:

Prebiotics help grow the good gut bacteria, which supports gut health. Prebiotics are also naturally found in fruits and vegetables such as berries, artichokes, broccoli, beans, lentils, bananas, and apples. These tend to be foods higher in FODMAPs so it’s tough for those with IBS and SIBO to tolerate enough prebiotic fiber.

Our favorite brand of PHGG is called SunFiber.  It’s a low-FODMAP type of soluble fiber that is typically very well-tolerated.  We always recommend starting with a very small dose and then gradually increase to the full dose (or your highest tolerated dose).

There are several additional studies showing the role of PHGG to help reduce symptoms of both IBS-associated constipation, diarrhea, and SIBO.

For constipation, one study showed those taking PHGG for 4 weeks had a significant improvement and reduced the need for laxatives and stool softeners(9).

For diarrhea, another study showed PHGG helps form the stool closer to a normal consistency(10).

If you suffer from IBS or SIBO, ask your doctor about PHGG.


Prebiotic supplements can cause gas, bloat, diarrhea, abdominal pain or reflux in large doses.  Again, this is why we recommend starting with a very small amount and gradually increase to the full dose.

3. Digestive Enzymes

Digestive enzymes are one of the best digestive health supplements, as they help digest protein, fat and carbohydrates. If the body is not making enough of them, which can be common with SIBO, it can lead to gas, bloating, and other uncomfortable digestive symptoms.

There are other specific digestive enzymes that can offer relief, depending on what your body may be deficient in. For example, those with lactose intolerance can benefit from an enzyme called lactase, and those with fat malabsorption can benefit from an enzyme called lipase.

How it works:

Digestive enzymes help properly break down your food, which reduces the chances of indigestion symptoms.

For example, a 2018 study showed those who took a digestive enzyme for 60 days had improved digestive symptoms. The participants suffered primarily from dyspepsia, another word for indigestion(11).


Digestive enzymes are generally safe. However, various digestive side effects are still possible, as well as swelling, asthma, or inflammation of the stomach lining.

Certain medications may also interact with digestive enzymes, such as diabetes medications(12).

Always speak to your doctor first before starting a new supplement to weigh the pros and cons.

4. Magnesium Citrate

This form of magnesium is one of the best supplements for digestive problems, particularly for  constipation. It can have a laxative effect and improve regularity.

How it works:

Magnesium citrate works for constipation by pulling water into the intestines. This water combines with dry stool, making it easier to pass and reducing uncomfortable strain.

As long as you don’t overdo it, magnesium citrate is gentle on the stomach and doesn’t typically cause urgent trips to the bathroom.


The most common side effects of magnesium citrate are diarrhea and stomach discomfort with large doses. Severe side effects are rare but possible such as dizziness, swelling, confusion, weakness, or heart issues(13).

Always speak to your doctor first before starting a new supplement to see what’s best for you.

How to Take Digestive Supplements

Just because a supplement is available to purchase over the counter doesn’t mean it’s safe and effective for you.  A supplement may be contraindicated with another supplement or medication. 

Best practices for taking a new supplement include:

  • Make sure these supplements are not contraindicated with your medical conditions, medications, other supplements and symptoms by checking with Medscape Interaction Checker.
  • Start one supplement at a time, to get a clear sense of what’s working, not working, and to ensure tolerance.
  • We recommend starting at the lowest dose and gradually increasing to your highest tolerated dose or the full dose.

Key Takeaways: Best digestive health supplements

Taking a digestive health supplement can be a great compliment to a complete gut healing protocol.

This is why we created our personalized gut healing program to relieve your symptoms faster and help you feel your very best.

You’re invited to save 15% on professional grade supplements.  These are the same supplements we use in our practice. 

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