Gluten-Free Macaroni and Cheese

Gluten-Free Macaroni and Cheese

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I decided to be brave today, and create my own gluten-free macaroni & cheese recipe from scratch :). I haven’t had homemade macaroni and cheese in over 3 years because of my newfound allergy/intolerance to milk and my sensitivity to gluten. Today was a bit on the chilly side, and I really craved some yummy comfort food to keep me warm. This gluten-free macaroni and cheese recipe blends in some elements of the traditional recipe made with a roux with almond milk and some nutmeg to round out the flavor. The result was a creamy and delicious macaroni and cheese sure to keep you warm! Also, this mac and cheese is not super thick, heavy, or ooey-gooey. There is some heft to it, but it is on the lighter side.

Gluten-free macaroni and cheese sits in a blue bowl on a blue and white checkered tea towel. A spoon sits to the right of the bowl. In the upper right is a glass baking dish filled with more macaroni and cheese. In the upper left is a cheese grater with a small brick of sharp cheddar.

Gluten-Free Macaroni and Cheese

This gluten-free macaroni and cheese recipe is amazing. The perfect comfort food to cozy up with on a cold night!
5 from 11 votes
Print Rate
Course: Dinner
Cuisine: American
Keyword: homemade mac and cheese, macaroni and cheese
Prep Time: 5 mins
Cook Time: 50 mins
Total Time: 55 mins
Servings: 6 people
Calories: 518kcal
Author: The Panicked Foodie


  • 10-12 ounces gluten-free macaroni (I've used gluten-free elbows and red lentil ziti)
  • 4 tablespoons butter of your choice (~2.1 oz in weight)
  • 2.1 ounces gluten-free all-purpose flour (~1/2 cup flour)
  • 2 cups milk of your choice
  • 2 cups grated extra-sharp cheddar cheese
  • 3/4 cup grated Parmesan cheese
  • 1 teaspoon ground mustard
  • 1/8 teaspoon nutmeg
  • Freshly ground Himalayan pink salt and freshly ground black pepper to taste


  • Bring a pot of water to a boil. Cook pasta until al dente, according to directions on the package. Drain pasta when finished cooking.
  • While the water is boiling, melt butter in another pot over medium heat. Once the butter is melted, add the flour. Mix with a wooden spoon to form a roux. While constantly stirring, cook the roux for 3 minutes (this will eliminate the flour taste in the final dish).
  • Add ~1/3 of the almond milk to the roux and mix until combined. Pour in another ~1/3 of the almond milk, mix until combined again. Then pour in the remaining almond milk and mix until everything is combined. You should end up with a thick soupy sauce.
  • Add both cheeses to the sauce. Continue stirring over medium heat until cheese is melted. You should end up with a thick sauce.
  • Add ground mustard and nutmeg to the sauce, stir until combined. If desired, add freshly ground Himalayan pink salt and freshly ground black pepper to taste.
  • Add the drained pasta to the pot with the cheese sauce and mix to coat the pasta. You can either serve the dish immediately as is, or…
  • Pour macaroni and cheese into a 9″ x 13″ pan and bake at 350F for ~30 minutes to infuse some crispness. You can also top with some panko bread crumbs or bacon prior to baking.


If you use 12 oz of pasta and don’t bake, you end up with a good pasta:sauce ratio. If you bake, you will end up with a thinner coating of sauce on the pasta. If you prefer a really thick macaroni and cheese, I would recommend going with 10 oz. of pasta.
Nutrition Facts
Gluten-Free Macaroni and Cheese
Amount Per Serving (0 g)
Calories 518
% Daily Value*
Fat 0g0%
Saturated Fat 0g0%
Trans Fat 0g
Polyunsaturated Fat 0g
Monounsaturated Fat 0g
Cholesterol 0mg0%
Sodium 0mg0%
Potassium 0mg0%
Carbohydrates 0g0%
Fiber 0g0%
Sugar 0g0%
Protein 0g0%
Vitamin A 0IU0%
Vitamin C 0mg0%
Calcium 0mg0%
Iron 0mg0%
* Percent Daily Values are based on a 2000 calorie diet. Nutritional information on The Panicked Foodie is provided as a courtesy and is approximate only. We cannot guarantee the accuracy of the nutritional information given for any recipe on this site.
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11 thoughts on “Gluten-Free Macaroni and Cheese”

  • I too have a very low tolerance for dairy. This sounds so delicious but I think it still might be too much cheese/butter for me 🙁

  • 5 stars
    Ooh this is such a great recipe. It is so awesome that this has no cows milk in it too which means everyone can enjoy the wonder that is mac n cheese!

  • 5 stars
    oh my God i love macaroni , it really is a splendid and sumptuous recipe but never have i tasted macaroni with cheese before thanks for the tips will try it later thanks for the tip

  • 5 stars
    I don’t have much of an intolerance to dairy however I do feel the affects when I have to much. I recently started replacing milk in my coffee with Almond Milk and I love it. Perhaps I will be brave and replace milk in this recipe as well. Thanks for being brave and trying out this recipe. I will keep it for future reference.

  • 5 stars
    Made this with almond milk and it came out amazing. I have never made a roux before so I wasn’t entirely sure how the end result would be, but the directions were straightforward and the end product tasted so good.

    • YES!! And once you’ve mastered that technique, you can use it as a basis for so many different things. Congrats, and I am glad you enjoyed the dish!!

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