Gluten is removed from food and drinks through several different methods depending on the product: mechanical separation, enzyme breakdown, membrane filtration, and distillation. Each approach works differently, and not all of them reduce gluten to safe levels for people with celiac disease. The method matters, and so does how the final product is tested.
Mechanical Separation in Wheat Starch
The oldest and most straightforward method is physically washing gluten away from starch. In industrial wheat starch production, flour is mixed with water to form a dough, then that dough is broken into smaller pieces by agitating it with more water. The mixture is passed over a fine mesh screen (about 150 mesh) that lets the liquid starch suspension flow through while catching the sticky gluten curds. The starch is then spun out of the liquid using a centrifuge and dried. The leftover gluten curds are shredded, washed again, and rescreened to refine them further.
This process takes advantage of gluten’s elastic, sticky nature. When hydrated, gluten proteins form a cohesive network that clumps together, making it relatively easy to separate from the granular starch particles suspended in water. The resulting wheat starch can be low enough in gluten to meet regulatory thresholds, though the final gluten content depends on how thoroughly the washing is done.
Enzymatic Breakdown
Enzymes offer a chemical route to breaking gluten apart. The most studied enzyme for this purpose is a prolyl endoprotease derived from the fungus Aspergillus niger, commonly called AN-PEP. It works by cutting gluten proteins at specific points, specifically behind proline residues, which are amino acids that make gluten so resistant to normal human digestion. The result is fragments of eight amino acids or smaller, pieces too short to trigger an immune response in people with celiac disease.
This enzyme works best in the acidic environment of the stomach, and in vitro studies have shown it can break down the specific gluten sequences (called immunogenic epitopes) that cause problems. Many over-the-counter “gluten digesting” supplements use a different enzyme called DPPIV, a dipeptidyl peptidase, but testing has found most of these products far less effective at destroying the harmful epitopes in stomach-like conditions.
In brewing, a similar approach uses a proline-specific endoprotease (sold commercially as Brewers Clarex) added at the start of fermentation. The enzyme breaks down gluten proteins in barley-based beer over the course of the brewing process. Beers treated this way are sometimes labeled “gluten-removed” rather than “gluten-free,” a distinction that carries real meaning for safety.
Membrane Filtration
Ultrafiltration uses physical membranes with precisely sized pores to separate molecules by weight. In liquid food processing, gluten peptides can be filtered through membranes with molecular weight cut-offs of 50,000 or 150,000 daltons. Proteins and peptide fragments larger than the cut-off get caught by the membrane, while smaller molecules pass through. This method is typically used alongside enzymatic treatment: enzymes first chop gluten into fragments, then filtration removes the larger pieces that remain.
Distillation Removes All Protein
Distillation is the most complete method of gluten removal and the reason spirits made from wheat, barley, or rye are generally safe for people avoiding gluten. The process works on a simple principle: liquid is heated, and only the components with low boiling points vaporize. That vapor is captured and cooled to become the distillate. Proteins, including gluten, have far higher boiling points than alcohol and water, so they simply don’t make it into the vapor. Assuming proper manufacturing practices, the distilled product contains no detectable protein at all. The FDA evaluates distilled products by testing for the absence of protein or protein fragments, rather than measuring gluten directly.
The Testing Problem With Processed Products
Verifying that gluten has actually been removed is harder than it sounds, especially in fermented or enzyme-treated foods. The industry standard test, known as the R5 sandwich ELISA (formally AOAC Official Method 2012.01), uses an antibody originally raised against rye proteins that binds to specific gluten sequences. This test works well across a wide range of foods, from baked goods and starches to meats, spices, and juices.
But it has a significant blind spot. When gluten has been partially broken down by enzymes or fermentation, the test can’t reliably measure what’s left. The fragments are too small or too altered for the sandwich format to detect properly. A newer competitive ELISA format using the same R5 antibody can detect smaller fragments, but current antibody-based methods still struggle to distinguish between different patterns of breakdown. Two beers treated with different enzymes might test similarly even though one contains more harmful fragments than the other.
This limitation has real consequences. In one study examining gluten-removed beer, sera from 31 active celiac patients were tested against barley extract, traditional beer, gluten-free beer (made from rice or other non-gluten grains), and enzyme-treated gluten-removed beer. None of the patients’ blood samples reacted to the truly gluten-free beer. But among the seven patients whose blood reacted to barley, four also reacted to traditional beer, and two of those reacted to the gluten-removed beer as well. The binding of residual peptides by celiac patients’ antibodies, but not by non-celiac controls, suggests that enzyme treatment may leave behind fragments that are still recognizable to a celiac immune system.
How Labeling Rules Handle the Gap
The FDA defines “gluten-free” as containing fewer than 20 parts per million of gluten, a threshold also used by the international Codex Alimentarius. But for fermented and hydrolyzed foods where standard testing falls short, the rules work differently. Manufacturers of these products must keep records demonstrating that all ingredients were gluten-free before fermentation or hydrolysis began. They also need to document that they’ve assessed the risk of cross-contact during manufacturing and taken steps to prevent it.
This records-based approach exists specifically because no current analytical method can reliably quantify gluten after it’s been partially broken down. For distilled products, the FDA takes yet another approach: they verify the absence of any protein in the distilled portion, since proper distillation should leave none behind.
Products made from gluten-containing grains and treated with enzymes (like gluten-removed beer) occupy an awkward regulatory space. Some brands use the term “crafted to remove gluten” rather than “gluten-free.” For people with celiac disease, the safest choice remains products made from inherently gluten-free ingredients, since the testing limitations mean enzyme-treated products from wheat, barley, or rye can’t be verified to the same standard.