Breakfast
Freeflourish
Gluten-Free Classic Baked Macaroni and Cheese
By Freeflourish Test KitchenReviewed by Freeflourish Editorial TeamPublished Apr 7, 2026 · Updated Jun 30, 2026
American
45 mins
glutenfreecomfortfoodfamilymealmaincoursedairyfreeoptionseasybudgetfriendlyquickrecipes
Enjoy this creamy, cheesy gluten-free baked macaroni and cheese—a comforting and family-friendly main course perfect for quick and easy dinners. Easily customized with dairy-free and budget-friendly options, this recipe is sure to please all ages.
Prep
15 min
Cook
30 min
Total
45 min
Servings
6
Difficulty
easy
Cuisine
American
Ingredients
Servings
6
- 12 ounces gluten-free elbow macaroni or cavatappi pasta
- 4 tablespoons unsalted butter (or dairy-free butter substitute)
- 1/4 cup gluten-free all-purpose flour blend
- 3 cups whole milk (or unsweetened plant-based milk for dairy-free)
- 1 cup shredded sharp cheddar cheese
- 1 cup shredded mild cheddar cheese
- 1/2 cup shredded mozzarella cheese
- 1 teaspoon Dijon mustard
- 1/2 teaspoon garlic powder
- 1/2 teaspoon onion powder
- 1/2 teaspoon smoked paprika
- 1/2 teaspoon salt, or to taste
- 1/4 teaspoon freshly ground black pepper
- 1/2 cup gluten-free bread crumbs (optional for topping)
- 1 tablespoon olive oil or melted butter (optional for topping)
Instructions
-
Preheat your oven to 350 degrees F (175 degrees C). Grease a 9x13 inch baking dish and set aside.
-
Bring a large pot of salted water to a boil. Add the gluten-free pasta and cook according to package directions until al dente, about 7-9 minutes. Drain and set aside.
-
In a large saucepan over medium heat, melt the butter. Once melted, whisk in the gluten-free flour blend to form a smooth roux. Cook, whisking constantly, for about 2 minutes without browning.
-
Gradually whisk in the milk, ensuring no lumps form. Continue cooking and whisking until the sauce thickens and coats the back of a spoon, about 6-8 minutes.
-
Remove the sauce from heat and stir in the Dijon mustard, garlic powder, onion powder, smoked paprika, salt, and black pepper.
-
Add all the shredded cheeses to the sauce and stir until melted and smooth. Adjust seasoning if needed.
-
Add the cooked pasta to the cheese sauce and stir gently to combine.
-
Pour the cheesy pasta mixture into the prepared baking dish and spread evenly.
-
If using, mix gluten-free bread crumbs with olive oil or melted butter and sprinkle evenly over the top for a golden crust.
-
Bake uncovered in the preheated oven for 25-30 minutes, or until bubbly and the topping is golden brown.
-
Remove from oven and let stand for 5 minutes before serving. Enjoy warm as a comforting gluten-free main course!
Tips
Allergen Overlap Note
Use certified gluten-free pasta, flour blend, and breadcrumbs, and check cheese, Dijon mustard, spices, and plant-based swaps for gluten-free labeling. Boil the pasta in a clean pot and use a clean casserole dish, since shared strainers, wooden spoons, or breadcrumb containers can carry wheat crumbs.
Texture Expectations
The pasta should stay tender but not mushy, with a creamy sauce and a lightly crisp top if using breadcrumbs. Cook gluten-free pasta just to al dente, whisk the roux until smooth before adding milk, and let the casserole rest 5 minutes so the sauce settles without becoming dry.
Dining With Non-GF Family Note
Serve this macaroni and cheese with its own spoon and keep regular rolls or wheat-based sides away from the casserole dish. If making both gluten-free and regular versions, label the gluten-free pan clearly and plate it first with clean utensils.
Frequently Asked Questions
- Can I make this macaroni and cheese dairy-free?
- Yes. Use dairy-free butter, unsweetened plant-based milk, and a meltable dairy-free shredded cheese. The sauce may be slightly less stretchy but should still be creamy.
- Why did my gluten-free pasta get soft?
- Gluten-free pasta can overcook quickly. Boil it only to al dente because it will keep softening while it bakes in the cheese sauce.
- Can I skip the breadcrumb topping?
- Yes. The casserole will be softer and creamier on top without breadcrumbs. You can also use crushed gluten-free crackers for a crunchy topping.
Ingredient Replacements
This Gluten-Free Classic Baked Macaroni and Cheese recipe is versatile and easily customizable to fit various dietary choices. Consider these ingredient substitutions to suit your needs:
- Gluten-Free Pasta: Substitute with any gluten-free shape such as penne, rotini, or shells for variety.
- Dairy-Free Butter: Use plant-based or vegan butter alternatives like Earth Balance or coconut oil to keep it dairy-free.
- Gluten-Free Flour Blend: Swap with grain-free flours like almond or cassava for a paleo or grain-free diet.
- Milk: Replace whole milk with unsweetened plant-based milks including almond, oat, soy, or cashew to make it dairy-free and vegan friendly.
- Cheese: Use dairy-free shredded cheese alternatives made from cashews or coconut oil for a vegan or dairy-free option.
- Gluten-Free Bread Crumbs: Try crushed gluten-free crackers or omit topping for grain-free or lower-carb versions.
- Thickener: For gluten and grain-free sauce thickening, substitute arrowroot powder or tapioca starch instead of flour blends.
These substitutions preserve the creamy, comforting qualities while respecting dietary restrictions, making this recipe ideal for family meals, meal prep, holiday and seasonal dinners, and budget-sensitive cooking.
Storage and Reheating
Store leftovers in an airtight container in the refrigerator for up to 4 days. Cool the casserole before covering so condensation does not make the topping soggy.
Reheat individual portions in the microwave with a splash of milk, or warm a covered baking dish in a 325 degrees F oven until hot. Use clean gluten-free containers and utensils for leftovers.
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