Enzyme Supplements: Uses, Suggestions, and Alternatives

Enzyme word cloud conceptFew would disagree that a Primal way of life advocates simplicity above all else. Nutritious foods, strategic movement, and an aversion to stress bordering on (healthy) obsession.

This “simple is good” mentality works swimmingly most of the time. Aligning our lifestyle to our evolved biology allows us to achieve a modern semblance of that all-important homeostasis, and I generally see no reason to tinker if it ain’t broke.

But, unfortunately, it’s not always black and white….

Monoculture continues to favor size and sexiness over nutrient density in our agricultural system, making it harder for us to extract the vitamins and minerals we need from the food we eat. And these days, life tends to include more sitting and stress than we can always fend off, regardless of our good strategies and intentions. 

This leads to something of a dilemma: subsist on simplicity and shake your head at the non-purists, or supplement to fill in the gaps of your otherwise stellar Primal pursuits. Digestive enzymes are one such gap filler, boosting digestive efficiency and ensuring greater nutrient absorption.

I’ve mentioned enzyme supplements on occasion in the past, and plenty of Primal folks have raised questions about them from time to time.

The Big Picture on Enzyme Purpose

Enzymes can be grouped into three broad categories: digestive enzymes, metabolic enzymes, and food-based enzymes. Digestive enzymes, the types you’ll see as enzyme supplements in your supermarket or health store, receive the lion’s share of our attention. As you can probably imagine from the name, they catalyze the breakdown of food into smaller, more absorbable molecules. 

The enzyme supplements you buy in-store are copies of the enzymes your body produces in-house. The pancreas is where most of the enzyme production takes place, but there’s also a decent amount released in saliva and in the stomach. These enzymes facilitate the biochemical reactions in the GI tract that physically enable the body to utilize the nutrients we eat, helping to save energy in the process.

Whereas digestive enzymes spend their days outside of cells, metabolic enzymes work their magic from inside cell walls. Once again, the pancreas is where it’s at for metabolic enzyme production, whereupon they set to work ensuring cell replenishment and reproduction.

The final frontier for enzymes is those that aren’t produced inside the body at all, but are in fact present in the foods we eat. When you hear raw food advocates talking about how heating consumables destroys the enzymes in those foods, these are the enzymes they’re defending. And they’re not wrong: raw foods contain far more enzymes than those that have been fried, baked, grilled or nuked. 

Many nutritionists in this camp believe that the majority of the food we eat should be raw, purely based on the premise that these food-based enzymes really give the digestive system a helping hand. Consuming more of these enzymes eases the pressure on internal enzyme production, ensuring more efficient digestion and preventing depletion of metabolic enzymes in the pancreas. I don’t offer this to say you shouldn’t ever cook your food (I’m not a raw food advocate and enjoy a mix of cooked/uncooked food each day.), but it does illuminate the power of enzymes for digestive health and nutrient absorption.

When It All Goes Wrong

Most people who switch over to paleo or Primal assume that their digestive issues will melt away, never to return again. The problem is, they’re generally transitioning from a diet steeped in ultra-heated, ultra processed foods with virtually no intact enzymes.

As a result, their systems bear the burden and exhaustion of low food-based enzyme input, chronically elevated cortisol, food intolerances, GI inflammation, and perhaps low stomach acid. Throw in an autoimmune disease and almost guaranteed gut inflammation, and their digestive health will undoubtedly be less than ideal. 

In response, enzyme supplementation might be an effective strategy for those who struggle with digestion, particularly in the transition to a healthy, whole foods, Primal diet. 

Where Enzymes Can Help

Researchers have uncovered a whopping 3000 or so varieties of enzymes, but those same folks humbly admit there may be as many 50,000 still to uncover.

Exogenous (a.k.a. lab-created and orally-supplemented) enzymes have been used to good effect in treating lactose intolerance and celiac disease, regulating testosterone, and plenty more besides. In many cases, patients who supplemented with digestive enzymes to treat a given malaise were able to wean themselves off enzyme supplementation after a time and continue on their way, symptom free.

Surprisingly, many of these same enzymes have also demonstrated the impressive ability to speed recovery and muscle damage after intense exercise, lower inflammation, and ease pain. But that’s a whole new kettle of fish and one which merits its own dedicated post.

In any case, these were specific digestive enzyme supplementations for clearly-defined health problems. Things get a little murkier when examining the average consumer suffering from the odd bout of gas or less-than-ideal stool.

As is always the case, everyone is somewhat different in their responses.

First, know that certain enzymes fulfill different roles in the GI tract. The big players are:

  • Protease, for breaking down protein
  • Lipase, for fats
  • Amylase, for carbs
  • Cellulase, for fiber
  • Lactase, for lactose
  • Maltase, for conversion of complex sugars to glucose
  • Sucrase, for most other sugars
  • Phytase, for B-vitamin conversion and all-round digestive goodness

That’s a lot to take in, and there’s more nuance to it. Nonetheless, if you wanted to apply it 100% literally, it could look like this…. 

Eating more fatty meat these days but not feeling like it’s settling well? Maybe step up the protease and lipase supplementation. Suspect you have lactose intolerance? Lactase enzyme supplementation might be just the ticket. Not sure what your problem is, but your stomach doesn’t seem to appreciate food right now? A broad-spectrum enzyme supplement containing all of the above is probably your best bet. 

But let me stress—I don’t believe enzyme supplementation should be a stand-in for personal experimentation with dietary particulars. The fact is, some of us do better without certain items in our diets, lactose being one. Others may be able to eat a little of everything but thrive more with adjusted proportions. Enzyme supplementation, particularly as a short-term strategy, can be one tool in your dietary attunement.

Personally, if you’re not able to drill down and identify your digestive Achilles heel but want to give enzymes a go, I’d probably try the broad spectrum approach. Even if you don’t necessarily need to top up concentrations of a certain enzyme in your GI, short-term enzyme supplementation isn’t likely to produce any side effects. Find a supplement that offers decent levels of the enzymatic big players along with betaine HCL, which can aid stomach acidification and hence improve digestion, and you might actually look forward to meals again.

It’s also worth knowing that your enzyme supplement in question could be sourced from one or more of 4 “parents”: plant, animal, bacteria and fungus. Because they’re cheaper to produce and a whole lot less volatile, fungal and bacterial enzyme sources are many times more common than those from plant and animal sources.

That being said, certain plant enzymes like papain and bromelain are now gaining popularity—likely in part because they’re more marketable, but also because they have a wider pH tolerance. Animal-derived enzymes have also historically been used to good effect in the treatment of certain disorders, most notably pancreatic insufficiency.

Unless you can find a plant enzyme supplement that ensures fortification from the ravages of stomach acid via a good enteric coating, fungal enzymes are a good bet.

Dosage and Quality Considerations


As far as supplements go, orally administered enzymes are pretty darn safe. Toxicity complications usually don’t arise unless a person is repeatedly knocking back well over the recommended dosage, and even then the side effects are typically limited to gastrointestinal upset. Robb Wolf has mentioned that in times of GI distress, he’d start off at a dosage 6 capsules (3 times the usual recommended dose) then work his way back down. I’ve talked to others, particularly those who’ve had a gall bladder removed, who take much more than that without issue. That said, there’s no reason to take more than you truly need for the results you want. 

Most cases of enzyme supplementation gone wrong can usually be traced back to extreme food sensitivities: classic examples include allergic reactions to porcine substances, bromelain or Aspergillus species. This probably comes back more to the quality of the enzyme supplement producer than the enzymes themselves, whereby shoddy QA/QC might not catch metabolites and by-products that could adversely react with the consumer…all the more reason to seek out a reputable brand.


Products that offer enzyme supplements from sources that are pH-tolerant and less likely to become denatured in harsh environments can negate the need for enteric coatings and are generally more stable in any case. As mentioned earlier, certain plant-sourced enzymes like papain can tolerate a wider pH range, but fungal enzymes are generally more resistant, have a broader spectrum of application, and don’t rely on enteric coatings to do their thing.

As an aside, if you’ve set your sights on a more fragile plant or animal-sourced enzyme, choosing a product that contains decent amounts of betaine HCL may be a good bet: the HCL helps your stomach to maintain consistently low pH levels, which should ensure the enzyme coating remains intact.


This is where things get a little complicated. Virtually all supplements (with perhaps the exception of probiotic cultures) are based on a weight-defined system, be that milligrams (mg), micrograms (mcg) or otherwise. This makes sense when it comes to vitamins and minerals, as weight is directly proportional to the amount of the compound in question.

Not so with enzyme supplements. As Ben Greenfield has said, enzymes are more accurately measured by units of activity and potency rather than unit weight. With this in mind, judging the potency of an enzyme blend can be achieved not by noting how many milligrams there are of each strain, but how many Food Chemical Codex (FCC) units each strain presents. Common FCC units of measurement include HUT (Hemoglobin Unit Tyrosine base) and USP (United States Pharmocopia).

Compare FCC units of individual enzymes (i.e. protease, lipase, etc.) to get an idea of which is most potent. But remember that potency doesn’t always imply quality, and that starting at a lower dose then working your way up is probably a wise course of action.


Back to simplicity. You likely know the drill for seeking out high quality supplements: avoid those undesirable “other ingredients” like gluten, dairy, cornstarch, soy and ambiguous compounds like “tablet coating.” Those with suspected food allergies should be pickier with these additives than others, and don’t be afraid to shop around.

Digestive Enzyme Alternatives

I’ve certainly got no issue with enzyme supplementation (I include a digestive enzyme formula in the Primal Master Formula), but if you’re looking for alternatives then there are plenty of options.

As I mentioned earlier, aiming for more food from raw sources is a critical part of realigning your digestive efficiency. But within that raw food spectrum are certain enzymatic powerhouses that could provide an alternative almost as powerful as dedicated enzyme supplements.

Papaya and pineapple, as the respective sources for the enzymes papain and bromelain, are a good start. Both papain and bromelain are proteolytic enzymes that efficiently break down long-chain proteins into simpler forms, making their parent fruits a good choice for the average Primal meat-eater. Other potent sources of plant-based enzymes include kiwifruit, avocado, and raw honey. Coconut oil and extra virgin olive oil also purportedly aid internal enzyme production.

I haven’t seen enough evidence to support the claim that raw meat and raw dairy products provide digestive enzymes that our own body can utilize, but there are other reasons why it might be worth giving either a shot anyway.

Beyond enzyme-rich foods, there are other easy steps you can take to support your body’s enzyme production and to streamline digestion in general. As you already know, leafy greens should be a significant part of each day’s Primal vegetable intake, but here’s another reason to give yourself a generous heaping: those greens contain ample cellulose, which attaches to toxic bile and keeps it moving out the back door. Cinnamon, or so the research would have us believe, performs a similar bile acid-binding role.

If general digestive upset is your problem, upping your bone broth consumption is also probably a good idea. The proline and glycine present (especially if you make your own extra-strong batches at home or use a quality collagen supplement) help to alleviate inflammation in the GI tract and regulate digestion, while the ample nutrients in a good cup of broth help to restock your reserves and rebuild damaged intestinal walls.

Finally, if your digestive issues are being caused by low stomach acid (this is more common than you think), you can try using a betaine HCL supplement short-term or employ natural alternatives if you prefer. Try 1-2 tablespoons of either raw apple cider vinegar or fresh-squeezed lemon juice in a glass of water before meals to stimulate your stomach’s digestive juices and minimize gaseousness post-feast.

And, of course, don’t forget ample prebiotic and probiotic sources in your diet for overall gut biome health

Thanks for reading, everyone. Do you supplement with enzymes? What’s been your experience with them? Any particular products or blends you’d recommend? Be sure to share your thoughts below.


About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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