Can Digestive Enzymes Help Food Intolerance?

Around 15-20% of the population has food intolerance. If you’re one of those, you know how it can drain the pleasure from food and make your food-world black and white.

But don’t worry — this article will walk you through a popular solution for food intolerance - digestive enzyme supplements.

So let’s take a look at what food intolerance really is (many people are still confused!), what digestive enzymes are, and whether they help with food intolerance.

What is food intolerance?

Food intolerance is a condition where your body can’t either break down a particular food molecule or is hypersensitive to it.

If you have food intolerance, you may experience the following symptoms after eating: 

  • Bloating
  • Tummy pain
  • Diarrhea
  • Excessive gas
  • Headaches

That’s because as undigested food molecules make their way to the large intestine, they meet a huge colony of bacteria waiting to munch on them. Bacteria ferment these molecules and produce gas in the process, which leads to uncomfortable symptoms.

Now, food intolerance is a general term. You’re not intolerant to just “food”. Instead, patients can’t break down (or are hypersensitive) to a very specific molecule in the food, which gives rise to several types of food intolerance.

Lactose intolerance

This is probably the most famous food intolerance and occurs when you lack an enzyme called lactase. Lactase breaks down the milk sugar lactose into smaller sugars glucose and galactose. These are easier to digest because they diffuse across the gut lining easily.

If you lack lactase, lactose will stay in the digestive tract where it will increase the water content (because it's osmotic) and lead to gas production. This causes stomach pain, bloating, spasms, and diarrhea.

Gluten intolerance

You must’ve also heard of gluten intolerance, which occurs when the body can’t handle gluten. Gluten is a protein found in barley, wheat, and rye. In addition to causing GI symptoms like gas and bloating, gluten intolerance can lead to:

  • Headache
  • Brain fog
  • Depression
  • Anxiety
  • Arthralgia (joint pain)

Fructose intolerance

Fructose is a sugar found in fruits, honey, and vegetables. And while fructose intolerance can occur due to a missing enzyme, it’s rare. More often, fructose intolerance occurs because the body can’t transport it across the gut lining. The transporter protein is missing, and this leads to fructose malabsorption. Symptoms include bloating, cramps, diarrhea, and a feeling of fullness.

Other types

Other types of food intolerance also exist but we won’t go into detail here. These include: 

  • Salicylate intolerance
  • Nitrate intolerance
  • Sulfite intolerance
  • Monosodium glutamate (MSG) intolerance 

Nitrate, sulfites, and MSG are usually found in food additives.

The role of digestive enzyme supplements in food intolerance

Since patients with food intolerance lack natural digestive enzymes (like lactase), supplementing them with synthetic enzymes can reduce their symptoms.

In the case of lactose intolerance, lactase supplements break down the sugar in your meal and reduce its delivery to the large intestine. This leads to less gas production and a relatively lower increase in the gut’s water content. Both of these factors help patients feel better. 

Enzyme supplements for other food intolerances work in a similar way but before you choose a supplement, it’s important to get a diagnosis of your specific condition. This will help you choose the right supplement.

While food intolerances need to be formally diagnosed by a doctor, you can aid your physician by maintaining a food diary. In a food diary, you note down what you ate, how much of it you ate, and how you felt after eating. After doing this for 1-2 months, you can review your diary with your doctor and see if you can identify a pattern.

It’s also important to note that digestive enzyme supplements are not stand-alone treatments for food intolerance — they work best in the context of a gluten-free or lactose-free diet to help patients deal with any “hidden” lactose and gluten found in food items.

Quinoa, amaranth, and red and black rice are good substitutes for gluten sources. 

For gluten intolerance, consider getting a combination supplement of protease (an enzyme that digests protein) and the gluten-digesting enzyme dipeptidyl peptidase IV.

Irritable Bowel Syndrome (IBS) and Food Intolerance

Digestive enzymes can be especially helpful in IBS patients because in these people, simultaneous food intolerances (particularly lactose intolerance) is very common. Combine food intolerance with IBS, and you get a really uncomfortable condition.

Apart from lactase enzyme supplements, FODMAP digestive enzymes can be helpful for IBS patients as they reduce the delivery of FODMAPs to the large intestine. This again reduces gas production and soothes uncomfortable GI symptoms that can follow a high-FODMAP meal.

Can enzyme supplements work for food allergies?

Enzyme supplements are not generally recommended for food allergies.  

While the symptoms of a food allergy are very similar to a food intolerance, the two are different disease processes. In food allergy, you’re not missing an enzyme. Instead, the body considers a molecule in the food (usually a protein) as “foreign” and launches an attack against it via the immune system. This leads to symptoms that include itching, swelling, hives, anaphlaxis, etc. 

In contrast to food intolerance, symptoms in food allergy:

  • Begin almost immediately after eating
  • Are not related to the quantity of the food eaten — even minute quantities can trigger symptoms which can be extremely severe.

There are many factors that can trigger the immune system, but the size of the offending protein is an important one. The larger the size, the more likely is the immune system to spot it and go berserk.  Enzyme supplements (particularly proteases) can break down the offending protein into smaller fragments, which are more likely to slip under the immune system’s radar. But once again, if you have a food allergy and are considering an enzyme supplement, make sure to talk to your doctor first!


Yes, digestive enzyme supplements can help food intolerance by making up for missing enzymes. Missing natural enzymes are a common cause behind food intolerance. In addition to food intolerance, digestive enzyme supplements may be  useful in IBS. However, enzyme supplements are not generally recommended for food allergies. Before investing in a supplement, make sure to talk to your doctor!

Medically reviewed by Onikepe Adegbola, MD PhD 

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