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Written by: Dahlia Rimmon MS, RDN
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Medically reviewed by: Nesochi Okeke-Igbokwe, MD, MS and Taylor Berggren, MS, RDN
If you’ve ever wondered, “what do digestive enzymes do?” or considered how they stack up against probiotics, you’re not alone. Many people struggling with tummy troubles search for relief from those uncomfortable digestive blues and often find themselves weighing one supplement against the other. We’re breaking down the similarities and differences between the two and showing how digestive enzymes and probiotics can actually work together to support better digestion and overall health.
When you think about a “healthy gut,” you’re probably picturing smooth digestion, no bathroom drama, and feeling comfortable after you eat. So it’s no surprise that when your gut is out of whack, it can feel like your digestion is staging a full-on rebellion (bloated belly and all).
While most of us lump everything gut-related under “the stomach,” your digestive system is actually a complex network that stretches from your mouth to your anus. It’s made up of organs that work together to break down food, absorb nutrients, and eliminate waste. At the heart of it all are two key players: digestive enzymes, which help break down the food you eat, and probiotics, which keeps your gut ecosystem in balance.
In this article, we’ll break down the differences between digestive enzymes and probiotics, how each supports your gut, and help you decide which one (or both) is best for your digestive health.
What are digestive enzymes?
Digestive enzymes are non-living proteins that your body naturally produces to help break down the food you eat into smaller, absorbable nutrients. They’re released at various points along your digestive system—starting in your mouth and continuing through your stomach, pancreas, and small intestine. Their job is to break down these nutrients (carbohydrates, fat, and protein) into simpler forms that can be absorbed into your bloodstream and used for energy, growth, and essential body functions.
While our gastrointestinal tract produces several digestive enzymes, the most common ones are amylase, lipase, protease, and lactase. Here’s a simple breakdown:
Amylase
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Breaks down: carbohydrates into sugars
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Produced in: saliva and pancreas
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Helps digest: foods like bread, potatoes, and corn
Lipase
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Breaks down: fats into fatty acids and glycerol
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Produced in: pancreas
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Helps digest: foods like avocado, olive oil, and coconut
Protease
- Breaks down: proteins into amino acids
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Produced in: pancreas
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Helps digest: foods like chicken, beef, salmon, and eggs
Lactase
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Breaks down: lactose, the carbohydrate in dairy into glucose and galactose
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Produced in: small intestine
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Helps digest: foods like milk, yogurt, kefir, and cheese
Benefits of digestive enzymes
If you’re generally healthy and don’t have a diagnosed digestive condition, you probably don’t need to take over-the-counter digestive enzyme supplements. “The human body naturally produces sufficient digestive enzymes—such as amylase, lipase, and protease—to effectively break down carbohydrates, fats, and proteins,” explains Lila Rawlings, MS, RD at Pendulum Therapeutics. In fact, unnecessary supplementation could interfere with your body’s natural enzyme production or cause unintended side effects.
That said, if your body isn’t making enough digestive enzymes on its own, supplements can offer much-needed relief. Here are some important digestive enzymes benefits and how they can offer support during mealtime:
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Enhance digestion: Enzyme supplements can help break down carbohydrates, fats, and proteins more efficiently and make it easier for your body to absorb nutrients.
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Reduce digestive discomfort: Smoother, more complete digestion can alleviate digestive symptoms like bloating, gas, indigestion, and abdominal pain.
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Expand dietary choices: Enzyme supplements may make it easier to enjoy a wider variety of foods without the usual digestive troubles.
For the best results, take digestive enzymes at the beginning of your meal. This gives them time to mix with your food during digestion. For example, say you're sensitive to lactose and often feel bloated or gassy after eating dairy—but like to enjoy ice cream occasionally anyway. Taking a lactase enzyme supplement before you dig in might help you avoid that annoying, uncomfortable tummy churn.
It’s worth noting, too, that diet, regular aging, and certain medical conditions—including pancreatitis, lactose intolerance, congenital enzyme deficiencies, and celiac disease—can impair the body’s ability to produce digestive enzymes to the point of deficiency. If you’ve been diagnosed with a deficiency, your healthcare provider may recommend prescription digestive enzymes to help fill in the gaps and keep things moving smoothly.
What are probiotics?
Probiotics are living microorganisms (bacteria and yeast) that provide health benefits when consumed in adequate amounts. When balanced properly in the gut, probiotics help maintain digestive health, support the immune system and mental health, and produce substances that regulate hormones, blood sugar levels, and appetite.
Your gut microbiome is established in utero, when microorganisms pass from mother to baby. This early ”seeding’ of probiotics sets the foundation for long-term gut health, but it doesn’t stop there. Over time, you can continue to support your microbiome ecosystem by consuming probiotic-rich foods such as yogurt, kefir, and kimchi, or by taking probiotic supplements.
It’s important to continue enriching your gut microbiome. As you age, the gut-brain axis, which is the bidirectional communication system between the gastrointestinal tract and the brain, also shifts. “Aging can lead to changes in gut microbiota composition, affecting digestion, immunity, and even mood and cognitive functions,” explains Rawlings.
Benefits of probiotics
Not all probiotics are created equal, and different strains have been studied for their unique benefits. To get the most out of a probiotic supplement, pick strains that align with your specific health goals. Below are several aspects of health that probiotics may benefit, along with some well-researched strains that support them.
Digestive health
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Clostridium butyricum: This strain produces butyrate, a short-chain fatty acid (SCFA) that supports gut health and encourages the growth of other healthy bacteria. Butyrate also reduces intestinal permeability, which may help relieve uncomfortable digestive symptoms, like gas and bloating.
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Lactobacillus acidophilus: L. acidophilus produces lactic acid and hydrogen peroxide to foster a balanced gut environment. This strain can also help alleviate constipation and improve lactose digestion, easing bloating, diarrhea, and other symptoms of lactose intolerance.
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Bifidobacterium animalis: According to clinical trials, this strain may help speed up digestion, improve digestive comfort, and relieve abdominal distention.
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Bifidobacterium infantis: Often passed from mother to child during childbirth, B. infantis is an inherited microbe that helps break down complex carbohydrates that humans cannot digest. In doing so, it supports the production of SCFAs like butyrate, which serve as an energy source for other gut bacteria.
Immune health
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Key strain: Akkermansia muciniphila
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What it does: Strengthens the gut’s intestinal lining to help keep toxins, pathogens, and partially digested food particles from leaking into the bloodstream—an important factor in maintaining a healthy immune response.
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Other strains linked to immune health: Clostridium butyricum, Bifidobacterium infantis
Glucose metabolism
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Key strains: Akkermansia muciniphila, Clostridium butyricum
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What they do: Stimulate the production of SCFAs and the protein P9, both of which signal the body to release the hormone glucagon-like peptide 1 (GLP-1). GLP-1 plays a key role in digestion, appetite, and regulating glucose metabolism.
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Other strains linked to glucose metabolism: Clostridium beijerinckii, Anaerpbutyricum hallii
Metabolic health
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Key strain: Akkermansia muciniphila
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What it does: Contributes to metabolic function by strengthening the gut barrier integrity and modulating the body’s inflammatory responses.
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Other strains linked to metabolic health: Clostridium butyricum, Anaerpbutyricum hallii, Clostridium beijerinckii, Bifidobacterium infantis, Faecalibacterium prausnitzii
Skin health
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Key strains: Akkermansia muciniphila, Faecalibacterium prausnitzii, and Ruminoccocus
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What they do: May inhibit the growth of bacteria that contribute to skin issues through the gut-skin axis, a two-way connection that links your gut microbiome and skin.
Mood
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Key strain: Akkermansia muciniphila
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What it does: Influences mental health and stress through the gut-brain axis.
Are digestive enzymes the same as probiotics?
Not quite. While both digestive enzymes and probiotics support digestion, they work in very different ways. Digestive enzymes are non-living proteins that help digest food into nutrients your body can absorb. They do most of their work in the upper part of your digestive system—like the mouth, stomach, and small intestine. They’re often used to help with specific issues, like lactose intolerance or enzyme deficiencies.
On the other hand, probiotics are living microorganisms that colonize the lower digestive tract (large intestine). They don’t directly break down food the way enzymes do, but instead help keep your gut microbiome balanced, support overall gut health, and influence several psychological pathways.
Can you take digestive enzymes and probiotics together?
Yes, you can take digestive enzymes with probiotics as part of your digestive health routine. The two work together to create an ideal environment in the gut where probiotics can thrive. Enzymes start the digestion process by breaking down food in the upper gastrointestinal tract. Probiotics finish the job by fermenting certain food components in the lower part. “Better digestion in the upper GI tract may reduce the burden of undigested food reaching the large intestine, creating a more balanced environment for probiotic bacteria,” explains Alayna Hutchinson, MS, RDN at Pendulum Therapeutics.
You can take digestive enzymes daily or as needed. Some people take them with heavier meals to help their body break down food more efficiently. For probiotics, consistent daily use is ideal to help maintain a healthy balance of good bacteria in your gut.
Probiotics or digestive enzymes: which do you need?
Choosing between digestive enzymes, probiotics, or both comes down to your symptoms, health conditions, and wellness goals. Here’s a simple guide to point you in the right direction.
If you have:
- Frequent bloating or digestive discomfort after eating certain foods
- Undigested food particles in your stool
- Conditions that affect enzyme production, e.g. pancreatic insufficiency, cystic fibrosis, or chronic pancreatitis
Try: Digestive enzymes
If you have:
- Recently taken antibiotics or have a history of frequent antibiotic use
- Intense food cravings
- Irregular bowel movements like chronic constipation or diarrhea
- Diagnosed irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD)
- Immune system challenges or frequent infections
- Signs of intestinal permeability issues (“leaky gut”)
Try: Probiotics
If you have:
- Tried enzymes or probiotics but only saw partial improvement
- Complex conditions that affect both upper digestive processes and lower gut health
Try: Digestive enzymes and probiotics
Always consult your healthcare provider before starting any new supplements, especially if you have ongoing digestive concerns. They can administer diagnostic tests (like stool tests, breath tests, or specialized pancreatic function tests) to help determine your specific needs. Keep in mind that the most effective approach usually combines the right supplements with healthy dietary and lifestyle changes.
Choosing the best supplements
When it comes to choosing supplements, it boils down to what your body needs and what you want to achieve. The best digestive enzymes or probiotics for you will depend on your body and your health goals.
Look for targeted supplements
Pay attention to the claims on supplement labels and choose products that match your specific needs. If you have a known enzyme deficiency (like lactose intolerance) or consistently experience discomfort after eating specific foods, a targeted enzyme (like lactase) to help you easily digest those particular foods.
If you don’t have a diagnosed condition but often feel bloated, gassy, or uncomfortable after meals, a broad-spectrum enzyme might be a better fit. Broad-spectrum enzymes contain a mix of enzymes (like amylase, lipase, and protease) to help with general digestive issues or when you eat a variety of foods. Broad-spectrum enzymes are also a good choice if you’re unsure which foods are causing digestive issues.
For probiotics, check that the label lists live or active strains—these indicate the number of beneficial microorganisms present at the time of manufacture or ingestion. Just as important, pick probiotic strains that match your specific symptoms and health goals.
Do your research
Before choosing supplements for gut health, it’s important to research brands and how products are made. Reliable companies will be transparent about their ingredients, sourcing, and manufacturing practices, and the quality control steps they take to ensure their supplements are safe and effective.
Always choose supplements from a reputable brand that uses independent third-party testing. This kind of testing helps verify that what’s listed on the label is actually in the product and that it’s free from contaminants. High-quality supplements prioritize purity, safety, and transparency.
Keep in mind that many claims you’ll see on supplement labels aren’t regulated by the Food and Drug Administration (FDA).
Key takeaways
- Digestive enzymes are non-living proteins that break down food into nutrients the body can absorb and use.
- Probiotics are live microorganisms found in the gut that, when properly balanced, promote digestion, help absorb nutrients, and support the immune system.
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Digestive enzymes and probiotics work together to support digestion and relieve uncomfortable digestive symptoms.
- Digestive enzymes and probiotics are both essential for optimal gut function and long-term microbiome wellness.
FAQ
Is it better to take digestive enzymes or probiotics?
If you’re researching probiotics vs. digestive enzymes for your own supplement routine, the thing to keep in mind is that it’s not really about choosing one over the other. Each plays a different role in the gut and the two often work together to support your digestive health.
Who should avoid digestive enzymes?
Although digestive enzymes can help many people, certain groups should use them with caution or avoid them entirely. If you:
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Have allergies: Individuals with allergies to enzyme sources (pineapple and papaya are two common ones) should check supplement labels carefully to prevent an allergic reaction.
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Have active peptic ulcers: Enzymes may irritate the stomach lining and exacerbate ulcers.
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Take anticoagulants: Some enzymes can have mild blood-thinning effects that could interfere with your medication and increase the risk of bleeding
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Have a digestive or genetic condition: For example, people with Crohn’s disease, ulcerative colitis, or IBS have sensitive gastrointestinal systems—and adding enzymes without medical advice might make symptoms worse.
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Are pregnant or breastfeeding: Avoid enzymes unless recommended by a doctor, as there’s limited research on their safety during this time.
As a general rule, always consult your healthcare provider before starting a new supplement regimen. Same goes for children—check in with your pediatrician before offering digestive enzymes.
What is the best supplement for gut health?
If you’re looking for a supplement to improve your overall gut health, consider a probiotic supplement with the strains like Akkermansia muciniphila, Clostridium butyricum, and bifidobacterium infantis. These strains can strengthen the gut lining, reduce gut permeability, and could be a simple way to support both your microbiome and overall health.
When should digestive enzymes be taken?
Take digestive enzymes right before eating or with meals. That way, they’re ready to break down food when it enters your digestive tract. The exact timing can vary depending on the type of enzyme, and some specialized formulations may have specific instructions. As a general rule, always follow the manufacturer's directions for best results.
Content is for educational purposes only and has not been evaluated by the Food & Drug Administration. Statements and products are not intended to diagnose, treat, cure, or prevent any disease.
