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Which to choose: digestive enzymes or probiotics?

Last Modified: September 09, 2026

Diseases & Disorders, Family Medicine

This post was written by Naskar Perez, pharmacy student, and Monica Somerfelt, PharmD, BCACP, Pharmacy, Parkview Health.

If you have ever experienced bloating after a meal, stomach discomfort or irregular bowel movements, you may have wondered which over-the-counter options may help improve your digestive health. Digestive enzymes and probiotics are two of the most popular supplements for digestive health, but they work in very different ways. In this post, we discuss key differences between digestive enzymes and probiotics to help you choose the best solution for your individual needs.

What are digestive enzymes?

Digestive enzymes are proteins that our bodies produce to help break down food faster. The primary digestive enzymes include:

  • Carbohydrase: breaks down carbohydrates
  • Protease: breaks down proteins
  • Lipase: breaks down fats

Lactase is used to help break down lactose in dairy products and may be added to some digestive enzyme supplements. In contrast, alpha-galactosidase helps digest some complex carbohydrates in lentils and certain vegetables.

Digestive enzyme supplements can be appropriate for those with food intolerances and anyone with a medical condition that may reduce enzyme levels in the body.

What are probiotics?

Probiotics are live microorganisms that are often called “good bacteria” that live in your gut microbiome and have beneficial effects. They help maintain a healthy balance of gut bacteria to support digestion, immune function, and overall digestive health.

Common probiotics seen in supplements available over-the-counter include:

  • Lactobacillus: breaks down sugars and carbohydrates
  • Bifidobacterium: breaks down complex carbohydrates and fiber

Digestive enzymes vs. probiotics

Digestive Enzymes

Probiotics

Help break down food

Help maintain healthy gut bacteria

Work during digestion

Support long-term gut health

May provide immediate relief

May take several days or weeks to see benefits

Usually taken with meals

Often taken daily

 

Which one might be best for you?

Digestive enzymes may help if you:

  • experience bloating after eating
  • have gas after eating certain vegetables or lentils
  • have a diagnosed enzyme deficiency condition

Probiotics may help if you have diarrhea after taking antibiotics, occasional constipation or diarrhea or irritable bowel syndrome.

These two supplements act differently, so it may be appropriate to include both in your regimen. However, if you experience any persistent symptoms, reach out to your primary care provider for an evaluation to rule out any underlying causes that may require additional treatment. 

Final recap

Digestive enzymes help your body break down food, while probiotics support digestive health by promoting a healthy balance of gut bacteria. 

Keep in mind, these supplements are not interchangeable, but they can complement one another depending on your needs. If you are unsure which option is best for you, talk with your healthcare provider or local pharmacist to help guide your choice.

Parkview Outpatient Pharmacies and Specialty Pharmacy provide a wide range of prescription medications and individualized support for those with chronic and complex conditions. At select locations, we offer customized medication solutions, including compounding and flavoring, making it easier for patients to take their prescribed treatments.

For more information on pharmacy services, contact or visit a location near you.