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  • Writer's pictureMarissa Mekelburg MS, RDN, CLT, HHP

How Long Does Gluten Stay in Your System After You Stop Eating It?

Gluten is one of the most common food allergens that people are exposed to on a regular basis. For some, it's just an inconvenience; for others, it can be life-threatening. If you want to see symptom relief, how long does gluten stay in your system?

You may be wondering: if you're going gluten-free or have already done so, how long does gluten stay in your system after you stop eating it? It's important to know how long gluten stays in your body and what you should do about it.

This article will help answer that question and more!

a sunny field of wheat under a blue sky

Photo Credit: Polina Rytova on Unsplash

Real quick: what is gluten?

Gluten is a protein that naturally occurs in wheat, barley and rye. In people with celiac disease it can cause serious damage to the small intestine if consumed. For this reason, many people who have been diagnosed with this condition must go on a gluten-free diet for life.

This means avoiding foods that contain gluten: wheat (ALL forms including spelt, Eikhorn etc.), rye, barley and anything made from those grains...which is a lot, once you really start looking at labels.

If you don't have a reaction to gluten, there is no reason to avoid it.

Protein digestion

Gluten is an example of just one of the many proteins found in our food. And whether we’re talking about beans, eggs or gluten, digestion of proteins follows the same steps and timeline.

Proteins are enormous molecules that are made up of amino acids. Our body does the hard work of taking proteins apart into their individual parts so that they’re small enough to be absorbed in the small intestine.

The timing varies from one person to another, but in general, the digestion of proteins doesn’t take any longer than a day or two (1). So while non-expert bloggers are quick to claim that gluten will “remain in your system” for weeks or even months, it simply isn’t true.

What is true, however, is that the inflammation reaction to gluten can last for a very long time. Let’s talk about that fine print, now.

Three round wheat bread loaves on a floured tabletop

Photo credit: Wesual Click on Unsplash.

Lasting reactions to gluten

Your body having an overreaction to gluten – such as gluten intolerance – can last for a while, even if the protein is completely out of your system. This varies by person, but can last for weeks or even months.

This all depends on the degree to which your gut has been affected by the gluten, how thoroughly you’re able to remove all gluten from your diet as well as how well you’re nourishing your body with the right nutrients to be able to optimize recovery.

Who needs to avoid gluten?

There are a lot of people who need to avoid gluten, and how long they have to stay away from it will depend on how severe their reaction is. For some with milder symptoms or less-severe conditions like dermatitis herpetiformis (which causes skin problems), avoiding eating gluten for just three days can help clear up the issue.

If you have a diagnosis of any of the following conditions, you may need to avoid gluten for a time (long enough to reduce inflammation and heal leaky gut) or you may need to avoid gluten for life.

And while it can seem like food allergies and intolerances are the same thing, they actually aren’t. More on that here: Food allergies, food intolerance and food sensitivities...what's the difference?

What are the symptoms of gluten intolerance?

If you're having a negative reaction to gluten, what does that look like or feel like? It can be remarkably different from one person to the next.


If you're having a gluten allergy (which is quite rare and not to be confused with a wheat allergy) or celiac disease, you'll experience an immune response in your small intestine (2).

Symptoms of wheat allergy are like that to a peanut allergy:

  • Itchy mouth, lips or throat

  • Difficulty breathing

  • Headaches

  • Cramps, diarrhea

Celiac disease

Celiac disease is an autoimmune condition in which the body self-destructs and attacks its own living tissue. In this case, the immune system attacks the cells of the digestive system, causing damage. The damage can accumulate over time (and takes a while to heal, once the person has an accurate diagnosis and is able to fully eliminate gluten from his or her diet.)

Celiac disease symptoms can include (3):

  • Diarrhea and belly pain

  • Unintended weight loss

  • Nutritional deficiencies

  • Brain fog

  • Fatigue

And the last known reaction to gluten? Gluten intolerance, otherwise known as gluten sensitivity.

Gluten intolerance

If you're having a gluten intolerance the symptoms will involve how food makes you feel or how it affects other parts of your body like how well you sleep. Some people who are intolerant to gluten report issues with their digestion, just not quite as quickly as with an allergy (4).

Symptoms may include:

  • Bloating, belly pain, diarrhea

  • Headache and brain fog

  • Fatigue

  • Joint pain

  • Anemia

  • Depression

You may have noticed that some of the symptoms overlap. So, how do you know which condition you have related to gluten, if any?

How do you know if you have gluten intolerance?

While there is currently no one specific test available to determine gluten intolerance/sensitivity, if you have been tested for celiac and are negative then you can give the removal of gluten a try and see if you feel better. One thing to keep in mind though, is that gluten containing foods (such as wheat, rye and barley) are also high in the FODMAP fructan so it might be the FODMAP and not the gluten that is causing an issue.

Sometimes determining if there is a gluten intolerance requires looking at the big picture and working with a clinician that can help put the pieces of the puzzle together. For example, I use MRT testing, a blood test, to see how my clients are reacting to gluten-containing grains and other potential food offenders. I also use GI MAP to help identify if gluten may be an issue since it looks at markers such as zonulin and anti-gliadin IgA.

While intestinal biopsy is an option for testing to see if you have celiac disease, it isn’t an accurate measure for gluten sensitivity. Those with gluten sensitivity don’t have the same measurable damage to their intestine as those with celiac (5).

(P.S. This is why gluten sensitivity was considered to be a fake syndrome for so long - the usual testing wasn’t able to detect anything wrong. Turns out we just needed a different tool to be able to test for the different condition.)

How do you know if you have celiac?

There are three ways to test for celiac disease.

  • Do an intestinal biopsy to note the damage to your intestine

  • Do blood testing to look for the antibody to gluten

  • Genetic testing

If you are suspicious that you have one of the above three reactions to gluten, should you just stop eating it?

Should I just stop eating gluten?


Let me be crystal clear here: if you suspect that you have celiac disease, do NOT stop eating gluten before doing testing. The blood testing measures a reaction to gluten. If you’re not eating gluten, we cannot measure the reaction. This creates a “false-negative” test result. The test says that you do not have a reaction to gluten, but it isn’t actually true.

And without the reaction to gluten, you also will not be able to see the damage done with a biopsy (Or the biopsy will be skipped based on the false-negative reaction from the blood testing). If you have celiac disease, it's critical that doctors know how much damage your intestines have already sustained.[1] [2] [3]

When gluten enters the digestive system and starts its trip through the small intestine, a person with undamaged intestines might only experience mild bloating or discomfort at worst from eating too many noodles.

a wooden sign painted with the word stop. A lizard sitting on top.

Photo Credit: Jose Aragones on Unsplash

What if I have already stopped eating gluten?

Because the blood testing looks for markers that your immune system is responding to gluten, you won’t be able to measure them if you’ve been avoiding gluten for a while.

This means you cannot accurately test for a reaction to gluten without eating gluten.

Before you can do testing, you’ll need to eat gluten. I know that this can feel scary, but it is the only way to get accurate results.

The recommended gluten intake will range from 1-2 servings per day for 2-8 weeks before testing (6). Bread is usually one of the easiest ways to incorporate gluten into the diet before testing. For my clients, especially if you’re eating gluten for the first time in a while, I recommend eating spelt bread, or even spelt sourdough bread. Spelt contains gluten but tends to be a bit better tolerated.

I’m stopping gluten: how long will it stay in my system?

The gluten proteins themselves are only physically in your body for a day or two. Normal digestion is fast and efficient.

However, if you’re having an immune reaction to gluten, the inflammatory response to having eaten gluten can stick around for a while. Especially if your gut is damaged during the process, causing a leaky gut. You need to heal your leaky gut before you see the most complete remission of your symptoms.

Unfortunately, that isn’t a fast process either, but I can help make it as efficient as possible for you. How Long Does It Take to Heal a Leaky Gut?

Key takeaways: how long does gluten stay in your system

If you suspect that you’re having a reaction to gluten, keep eating it long enough to do thorough testing. While the treatment – avoiding gluten – may be the same, there is no reason to avoid gluten unless you’re 100% sure it is causing your symptoms.

If you’re ready to see remission from your digestive health issues, reach out! Get started by scheduling an initial visit.


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