Gluten-Free Macaroni and Cheese

Macaroni cheese

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Prep: 20 mins
Cook: 45 mins
Total: 65 mins
Servings: 6 to 8 Servings

Are you in need of comforting? This creamy and delicious gluten-free macaroni and cheese recipe should do the trick.

Homemade, fast and easy Mornay sauce—a traditional rich and creamy cheese sauce—is the key component to flavor in this wheat-free version of macaroni and cheese. Amaranth is the perfect wheat flour substitute for thickening the cheese sauce—it works every time.

If you're looking for a gluten-free/rice-free pasta, use a corn pasta like Sam Mills Pasta d'oro in this recipe.


  • 2 tablespoons butter (unsalted)
  • 7 tablespoons butter (unsalted)
  • 1 pound macaroni (gluten-free, cooked al dente)
  • 1 pinch salt
  • 4 tablespoons butter (unsalted)
  • 4 tablespoons amaranth flour
  • 2 cups milk (OR dairy substitute; light organic coconut milk works well)
  • 1 teaspoon salt (OR GF herbal salt)
  • 1/4 teaspoon pepper (fresh ground, or to taste)
  • 1 teaspoon onion powder (gluten-free)
  • 1/2 teaspoon garlic powder (gluten-free, not garlic salt)
  • Optional: 1 pinch cayenne (gluten-free)
  • Optional: 2 teaspoons Franks's Hot Sauce
  • 2 cups cheddar cheese (freshly grated)
  • 1 cup Parmesan cheese (freshly grated)
  • 1/2 cup Gruyère cheese (freshly grated or Swiss cheese)
  • 1/2 cup fontina cheese (freshly grated, or provolone or Havarti cheese)
  • Salt and pepper (to taste)

Steps to Make It

Prepare the Pan and Boil the Pasta

  1. Heat oven to 350 F. Put 2 tablespoons of unsalted butter in a 3-quart baking dish. Set aside.

  2. Fill a large stockpot half full with water. Cover and bring water to boil over high heat. 

  3. Add gluten-free elbow macaroni noodles and a pinch of salt and return water to a boil.

  4. Cook according to package directions, until al dente.

Make the Cheese Sauce

  1. While pasta is cooking, make the Mornay cheese sauce.

  2. Start with a roux by melting 4 tablespoons of butter in a medium saucepan over low heat. Whisk in amaranth flour and cook for 2 minutes, whisking constantly.

  3. Slowly whisk in milk or dairy substitute. Increase heat to medium and whisk until mixture thickens.

  4. Remove from heat. Add salt, pepper, onion powder, garlic powder, a pinch of optional cayenne, optional hot sauce, 1 cup cheddar cheese, 1/2 cup Parmesan cheese and all of the Swiss and fontina cheeses. Stir until cheeses melt and the mixture is smooth and creamy.

  5. Put the reserved baking dish with butter in the heated oven and leave just until butter melts. Remove and coat bottom and sides of the dish with butter using a pastry brush.

  6. Drain, rinse and pat dry cooked pasta. Pour half of the pasta into the baking dish and cover with about 1/2 of the cheese sauce. Distribute remaining pasta on top and evenly cover with remaining cheese sauce.

  7. Lightly salt and pepper and top with remaining 1 cup cheddar cheese and 1/2 cup Parmesan cheese. Bake for 45 minutes or until the top is golden and bubbling. Cool for at least 5 minutes before serving.

Note: Always make sure your work surfaces, utensils, pans and tools are free of gluten. Always read product labels. Manufacturers can change product formulations without notice. When in doubt, do not buy or use a product before contacting the manufacturer for verification that the product is free of gluten.