When & How to Take Digestive Enzymes
Written By Ana Aleksic, MSc Pharm

When & How to Take Digestive Enzymes

Low digestive enzyme production is one of the main causes of indigestion and poor nutrient status. Supplemental digestive enzymes may help improve digestion and general wellbeing if taken properly. This post dives into the “whys,” “whens,” and “hows” of digestive enzyme supplementation to help you get results. 

Disclaimer: This post is for informational purposes only. Digestive enzyme supplements have not been approved by the FDA for medical use. Speak with your doctor before supplementing.

How Digestive Enzymes Work

The basics

Digestive enzymes break down fats, proteins, and carbs into nutrients your body can absorb. Most digestive enzymes are made in the pancreas (Ianiro et al., 2016). 

Various factors can lower your production of digestive enzymes, including (Domínguez-Muñoz, 2007; Roxas, 2008; Rossi & Lentze, 1984; Kondo et al., 1988; Wydmanski et al., 2016; Kallegari & Lami, 1984):

  • Chronic pancreatitis (inflammation of the pancreas) 
  • Other disorders of the pancreas
  • Cystic fibrosis
  • Digestive disorders
  • Liver disease
  • Gut dysbiosis (poor gut microbiome health)
  • Diabetes
  • Obesity
  • Autoimmune diseases
  • Drugs (including chemotherapy)
  • Smoking 
  • Stress
  • Old age
  • Diet
  • Genetics

Our digestive enzyme supplement

Microbiome Plus+ Digestive Enzymes Supplement contains 18 plant-based enzymes that work synergistically (alpha-galactosidase, amylase, aspergillopepsin, beta-glucanase, cellulase, glucoamylase, hemicellulase, invertase, lactase, lipase, pectinase, peptidase, phytase, protease 1 and 2, xylanase, plus bromelain and papain).

Why take them

People who struggle to make enough digestive enzymes and suffer from indigestion may choose to supplement. The rationale is to provide your body with the amount of digestive enzymes it’s lacking to function optimally. Supplemental digestive enzymes may improve digestive, gut, heart, and joint health (Ianiro et al., 2016). 

Aside from supplementing with digestive enzymes, it’s important to optimize your diet and lifestyle and work with a practitioner to uncover the underlying cause of your issues.

To boost your digestive enzyme levels, keep active, add herbal bitters to your diet, and eat more foods rich in nutrients, enzymes, prebiotics, and probiotics (Koibuchi & Suzuki, 2014; McMullen, 2015; Conlon & Bird, 2015).  

If you’re ready to start taking a quality digestive enzyme supplement, follow the steps outlined below for maximum results.  

infographic, how to use digestive enzymes, 5 steps, with food images

1) Take Digestive Enzymes with Food

Digestive enzymes need to be taken with food to have an effect. Their role is to break down nutrients in food. There’s no point in taking them on an empty stomach—the enzymes will have nothing to “work on” (Roxas, 2008). 

It’s best to take digestive enzymes at the beginning of the meal. This ensures that the enzymes will efficiently mix with food in the digestive system, mimicking natural enzyme secretion. 

2) Combine with the Right Foods

Should I take digestive enzymes with specific foods?

In short, yes. 

To do this, you need to know what the main types of digestive enzymes are and what foods they can help you digest. Use the list of foods outlined below as a guide (Whitcomb & Lowe, 2007). 

Microbiome Plus+ digestive enzymes contain all the enzymes listed. 

Types of digestive enzymes & list of foods they act on

Proteases and peptidases

Proteases break down proteins into amino acids. 

Peptidases are involved in the final steps of protein digestion: they break down small peptides into amino acids (Kim & Erickson, 1985). 

Bromelain is a type of protease from pineapple. Like all proteases, it helps digest proteins when taken with meals. However, foods like potato and soy may reduce its activity (Valueva et al., 1997).

Papain is a protease extracted from the raw papaya fruit. It boosts the digestion of high-protein foods. No wonder chefs also use it as a meat tenderizer. Papain also has many other potential health benefits (Kong et al., 2021).  

Foods: meat, fish, eggs, and legumes. 


Aspergillopepsin is a protease from yeast that can break down dietary gluten into short peptides (unlike animal-based pepsin) (Ehren et al., 2009). 

Foods: wheat, rye, and barley. 


Lipases break down fats into fatty acids. 

Foods: any oil or fat. 


Amylases break down complex carbs into simple sugars. They include cellulase, hemicellulase, glucoamylase, invertase, alpha-galactosidase, beta-glucanase, pectinase, and xylanase. 

Alpha-galactosidase helps digest carbohydrates in beans that can cause flatulence, abdominal bloating, and stomach pain (Di Stefano et al., 2008).

Beta-glucanase works together with xylanase and cellulase to break down beta-glucan in cereal grains, wheat, and barley (Habte-Tsion & Kumar, 2018). 

Pectinase breaks down pectin, a soluble fiber found in many fruits and plants. 

Xylanase, cellulase, and hemicellulase also help digest high-fibrous plant foods like vegetables and whole grains (Chen et al., 2020). 

Foods: potatoes, grains, beans, pears, apples, citruses, broccoli, cauliflower. 


Lactase breaks down lactose, the main sugar in dairy, into simple sugars. People lacking this enzyme have lactose intolerance. 

If you’re intolerant to lactose, increasing your intake of fermented milk products like yogurt may also help. Studies show that yogurt high in lactic acid probiotic bacteria helps improve lactose absorption and reduce symptoms of intolerance (Ianiro et al., 2016).

Foods: yogurt, milk, soft cheese, and most dairy products


Phytase breaks down phytic acid, a plant-based anti-nutrient that can cause digestive upset. 

Foods: whole grains, beans, soy, peanuts, lentils, potatoes, beets, carrots, nuts, and seeds.

3) Adapt to Your Food Tolerance Level

Should I take digestive enzymes with every meal?

The digestive enzymes you take with a meal gradually get used up as they come into contact with food and travel down your digestive tract. 

When digestive enzyme production works perfectly in the body, each meal triggers the release of the right combination of digestive enzymes. Food gets maximally digested, nutrients get broken down and absorbed, and the whole cycle starts again with the next meal (Corring, 1980). 

You may not need to take digestive enzymes with every meal, depending on your food intolerances. Supplementation should mimic healthy digestion. To get into an optimal regime, you should ask yourself: 

  • Which foods always trigger my symptoms? 
  • Which foods am I usually intolerant to? 
  • How often do I eat these foods?

If you’re about to eat a meal that’s high in foods you don’t tolerate well, supplementing is usually a good idea. 

There might be only a couple of foods that you don’t tolerate and eat only occasionally. If so, you can take digestive enzymes only with those meals. 

On the other hand, you may have trouble digesting most foods that you eat on a daily basis. If that’s the case, you may want to take enzymes regularly with each meal. 

4) Dose to Your Needs

There is no standard dosage for digestive enzymes. Studies often use enzyme mixtures and dosages vary widely. Also, the dosage should be adapted to each person’s individual needs and diet. 

We recommend taking one capsule with each meal that contains foods you don’t tolerate well. 

5) Track Your Response

Clinical trials on digestive enzymes report results after 2-12 weeks, depending on health issues (Akhtar & Haqqi, 2012; Majeed et al., 2018).

We recommend regularly supplementing for at least two to three weeks if you have daily indigestion and don’t tolerate most foods.

6) Boost the Benefits with Probiotics & Prebiotics

Digestive enzymes work in synergy with probiotics and prebiotics

Probiotic gut bacteria produce digestive enzymes, while digestive enzymes enhance the activity of probiotic bacteria. Prebiotic fiber additionally feeds your probiotic bacteria, improving the overall health of your gut microbiome (Haq & Mukhtar, 2006)

Research confirms that adding probiotics to digestive enzymes may enhance the digestive and heart health benefits (Ianiro et al., 2016; Ichim et al., 2016). 

We recommend Microbiome Plus+ prebiotic and probiotic synbiotic formula as an add-on to digestive enzymes for optimal results. 

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Ana Aleksic, MSc Pharm

Ana is an integrative pharmacist and scientist with many years of medical writing, clinical research, and health advising experience. She loves communicating science and empowering people to achieve their optimal health. Ana has edited 800+ and written 150+ posts, some of which reached over 1 million people. Her specialties are natural remedies, women’s health, and mental health. She is also a birth doula and a strong advocate of bridging scientific knowledge with holistic medicine.

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Ana Aleksic

Statements made on this website have not been evaluated by the U.S. Food and Drug Administration. Information provided by this website or this company is not a substitute for direct, individual medical treatment or advice. It is the responsibility of you and your healthcare providers to make all decisions regarding your health. Microbiome Plus recommends that you consult with your healthcare providers regarding the diagnosis and treatment of any disease or condition. Products sold on this website are not intended to diagnose, treat, cure, or prevent any disease.

1 comment

Thank you for the wonderful information about your vitamins and what they will do for your health

Bernice McCrea

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