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This gluten-free Baked Macaroni and Cheese recipe is a crowd-pleasing favorite! Cheesy and creamy with a crunchy, buttery top, it’s everything baked mac & cheese should be.
I love Macaroni & Cheese, and you all must love it too – I get asked for mac & cheese recipes every time I teach a cooking class, and usually end up discussing it once or twice at Gluten-Free events, too.
- Apr 20, 2017 Super creamy gluten-free southern baked macaroni and cheese recipe loaded with three kinds of cheeses. The best gluten-free mac and cheese baked to perfection in just 20 minutes. Recipe originally published April 2017, photos and post updated September 2018.
- The gluten free cheese sauce that we use for queso is perfect for making macaroni and cheese. We discussed that method in that recipe, too. We discussed that method in that recipe, too. All it calls for is some freshly shredded cheese tossed in a bit of starch to help thicken the sauce (but without a roux), some milk, and some Kraft deli-style.
- Combine all of the ingredients in a food processor and pulse until well-combined, then set aside in a small bowl. Drain the Potatoes and Carrots, then set aside. Briefly rinse out the pot, then re-fill with water and bring to a boil again. Once boiling, add the Pasta and cook according to package instructions.
I usually start making Macaroni & Cheese as soon as the crisp Fall weather shows up, it just seems like the thing do to. This is my favorite basic baked version, but don’t be afraid to switch the cheeses up and make it your own: I’ve used every type of cheese under the sun, and have even used smashed potato chips when I was out of GF breadcrumbs. I’ve also made my famous Bacon Pimento Mac & Cheese with this topping, and it’s incredibly delicious too.
There are tons of gluten-free pastas on the market! I my current favorite is the fresh GF pasta from Manini’s (find it in the cold case at premium grocers) or the dried elbow pasta from Jovial.
Ingredients
- 1/2 pound Gluten Free elbow macaroni
- 3 tablespoons butter
- 3 tablespoons Gluten-Free Flour Blend, or 2 tablespoons rice flour + 1 tablespoon tapioca starch
- 1 1/2 tablespoons powdered mustard
- 3 cups milk
- 1/2 cup yellow onion, finely diced
- 1 teaspoon paprika
- 1 large egg
- 12 ounces sharp cheddar, shredded
- 1 1/2 teaspoons kosher salt
- Fresh black pepper
Optional Topping:
- 3 tablespoons butter
- 1 cup Gluten Free panko breadcrumbs or 1 cup rough-chopped Gluten Free croutons

Directions
Preheat oven to 350 degrees F.
In a large pot of boiling, salted water cook the pasta to al dente, careful to not overcook.
While the pasta is cooking, in a separate pot, melt the butter. Whisk in the Gluten Free flour and mustard and keep it moving for about five minutes, making sure the mixture is completely smooth. Stir in the milk, onion, and paprika. Simmer for ten minutes.
Temper in the egg. Stir in 3/4 of the cheese. Season with salt and pepper. Fold the cooked & drained macaroni into the mix and pour into a 2-quart casserole dish. Top with remaining cheese.
Topping: Melt the butter in a saute pan and toss the breadcrumbs to coat. Top the macaroni with the bread crumbs.
Bake for 35-40 minutes. Remove from oven and rest for five minutes before serving.
Notes

photo by the incredible James Collier. He always makes my food look fabulous.
Gluten Free Mac and Cheese is just the comfort casserole you're craving. This gluten free version will really make you smile.
Comfort food is called comfort food for a reason. For me gluten free mac and cheese is one of my favorites. I have a recipe that I absolutely love for gluten free one-pot, no-drain macaroni and cheese, but sometimes I just really want creamy cheesy noodles with crispy buttered breadcrumbs on top.
When I was about 8, I had an auto-immune illness that had me sick for several months. I still remember that moment when I finally felt good enough to eat. Of course I went right to my favorite comfort foods!

One of the first things that sounded good to me was macaroni with my mom's homemade cheese sauce. I remember eating those 'cheesy noodles', as we call them in our home now. Nothing beat finally feeling like a kid again! I remember I was running around and playing with my siblings as I left the dinner table after finishing a plate of homemade mac and cheese. One of my favorite memories!
My mom's homemade cheese sauce is super easy to make, and it is even better when you load the sauce and noodles into a casserole dish and top them with toasted breadcrumbs, butter, and of course MORE cheese.
Something else that I love about this gluten free baked macaroni and cheese is that you can really add whatever cheese is your favorite. Usually I use straight up cheddar, with maybe a little Monterrey Jack to make it a bit more gooey. You can even add a bit of cream cheese!
Just make sure whatever cheese you add is grated (or cut into small cubes if it is too soft to grate) and turn off the stove before you add it. Just let the residual heat in the sauce gently melt the cheese. Adding the cheese this way helps to prevent it from curdling, separating, or doing any manner of funky stuff. The cheese also melts better if you grate it yourself, then it isn't covered in that anti-caking powdery stuff which can cause aforementioned funky stuff to happen.
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Gluten Free Mac and Cheese Recipe
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Ingredients
- 1 pound Gluten Free Elbow Macaroni
- 1/2 cup Butter
- 3/8 cup Gluten Free Rice Flour, Or gluten free rice based AP blend without xanthan gum
- 4 cups Milk
- 1 teaspoon Dijon Mustard
- Salt and Pepper, To taste
- 3 cups Grated Cheese, About 9 ounces
- 3/4 cup Gluten Free Breadcrumbs, Homemade or store-bought
- 3 tablespoons Butter
Directions
- Cook the gluten-free elbow macaroni according to the package directions, to al dente.
- In a heavy bottomed saucepan melt the 1/2 cup butter and whisk in the flour. Continue to cook, while stirring, until the flour turns a nice golden brown. About 8-10 minutes.
- While whisking, stir in the milk. Add the mustard and season to taste with salt and pepper. Continue to heat stir until the sauce is thickened.
- Remove from heat and stir in 2 cups of cheese. Stir until melted.
- Lightly grease a casserole dish and spoon the noodles and cheese into it.
- Sprinkle the top with the seasoned breadcrumbs, drizzle with the melted butter, and top with the remaining 1 cup of grated cheese. Bake at 350 for 10-15 minutes or until the cheese is melted and the crumbs are crispy.
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Homemade Gluten Free Macaroni And Cheese Recipe
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- Published:
- Modified:
- Author:
- Brianna Hobbs
- Cuisine:
- Gluten Free
- Category:
- Gluten Free Baking
- Tags:
- Gluten Free, Gluten Free Baking, Casseroles, Easy Dinners, Macaroni and Cheese, Pasta, Cheese, Side Dishes
- Related Recipes:
- Gluten Free Recipes, Gluten Free Baking Recipes, Casserole Recipes, Easy Dinner Recipes, Macaroni and Cheese Recipes, Pasta Recipes, Cheese Recipes, Side Dish Recipes
- Recipe Yields:
- 8 servings
- Prep Time:
- Cook Time:
- Total Time:
- Related Post:
- Published:
Author:Brianna Hobbs
Recipe Yields:8 servings
Prep Time:30 minutes
Cook Time:15 minutes
Total Time:45 minutes