Can coffee cause stomach issues?

Katarina Mollo MEd, RDN, LDN
Q: Hello! My mother has celiac disease and is strictly on a gluten-free diet, yet she still has some stomach issues. This week I started reading about different people and articles saying that coffee could be causing that, as some coffee's might be cross-contaminated with gluten. Is that true? I can't find any scientific articles to test this theory out, but what I do find is many people online who claim switching over from processed coffee grounds to coffee beans has significantly helped them. I know coffee itself is gluten free but is there any truth to this?


Plain, traditionally brewed coffee is generally considered gluten-free. I am not aware of any tests that indicate that pure coffee contains gluten. However, getting whole beans and grinding them yourself would take a potential element of cross-contact out of the equation. Definitely avoid grinding coffee at a store, as there is potential for cross-contact with products containing gluten that have been used in the same grinder. Note that some flavored coffees may contain gluten ingredients, often from barley, so make sure to always read the label.

In addition, many people get IBS symptoms from coffee as it can irritate the GI tract and those symptoms can mimic celiac symptoms. Common things added to coffee such as sugar, milk/cream and flavored syrups can also trigger symptoms. Those additives can contain gluten as well so always check the label carefully of anything ingested even if it is in a beverage.

Aside from coffee there are also other issues your mother should explore concerning her symptoms and discuss with her healthcare provider. About 7-30% of people with celiac disease still have symptoms even though they are on a GF diet (1).

Here are the most common causes of not getting better after diagnosis:

Dietary indiscretion/inadvertent exposure to gluten (cross-contact and oats are common culprits, if she eats oats, review this information about oats:

Lactose intolerance, fructose malabsorption or other carbohydrate intolerances (such as high FODMAPs)

Small intestinal bacterial overgrowth (SIBO)

Other food allergies/intolerance (dairy, soy, corn, etc.)

Pancreatic enzyme deficiencies

Microscopic colitis

Refractory CD which may require steroids (very rare) (2)

Again, all of the above should be discussed with your mother's healthcare provider.


  1. Kelly CP, Bai JC, Liu E, Leffler DA. Advances in diagnosis and management of celiac disease. Gastroenterology. 2015;148(6):1175-86.
  2. National Celiac Association. Gluten-Free, Off to A Fresh Start. Presentation. Updated May 4, 2018.

Note: This information is provided by NCA and Katarina Mollo MEd, RDN, LDN, NCA's Director of Education. This information is meant for educational purposes only and is not intended to substitute for personalized medical advice or replace any medical advice provided directly to you by your health care provider. No liability is assumed by the NCA or Katarina Mollo, MEd, RDN, LDN by providing this information.

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