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    Home / Recipes / Main Dishes

    The Best Baked Mac and Cheese Homemade: Gluten-Free

    Posted On Jan 12, 2023 · Updated On Jan 16, 2023

    The Best Baked Mac and Cheese Homemade: Gluten-Free

    This recipe for Baked Gluten-Free Macaroni & Cheese is next-level delicious.

    Kid ZoneMain DishesRecipes & Techniques by Cooks We LoveThis Is SO GOOD.

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    Mmm… macaroni and cheese- one of those meals that can be made in a variety of ways. Honestly, I can think of 50 ways right now! I love all virtually all versions of gluten-free Mac n' Cheese, but Baked Mac and Cheese homemade is my absolute favorite! Cheesy & creamy with a crunchy, buttery top, it's everything baked macaroni & cheese should be.

    Every time I give a cooking class, I'm asked for mac & cheese recipes, and I generally end up talking about it once or twice at gluten-free events. I adore mac & cheese, and I'm guessing you all do, too, since you're reading this recipe.

    3 bowls of mac & cheese with side salads on a grey background

    Can I use different cheeses in this recipe?

    This basic baked version of mac n cheese calls for Sharp Cheddar. Feel free to experiment with different cheeses and customize it to your tastes. A blend of Sharp Cheddar and Gruyere is fabulous. I also often toss in some Parmesan as well.

    How long does this mac n cheese take to make?

    It takes about an hour to make this mac and cheese homemade, but man it is worth it! About 15-20 minutes of that is active cooking time, the balance is for baking.

    Close up of a bowl of mac & cheese with a side salad all on a grey background

    What types of cheese is used in this recipe?

    This recipe calls for sharp cheddar cheese, 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.

    Which pasta should I use for gluten-free macaroni and cheese?

    The best choice for gluten-free mac and cheese recipes is fresh gluten-free pasta. Our favorite is from Manini’s (find it in the cold case at premium grocers). You can also use dried gluten-free elbow pasta, we like the ones from Schar, Barilla or Jovial. Our favorite pick for cassava flour pasta is Jovial.

    You can also use conventional pasta in this recipe if you aren't gluten-free.

    What ingredients are in this recipe?

    • Gluten-Free elbow macaroni
    • Butter
    • Gluten-Free Flour Blend, or rice flour + tapioca starch
    • Powdered mustard
    • Milk
    • Yellow onion
    • Paprika
    • Egg
    • Sharp cheddar
    • Kosher salt
    • Fresh black pepper
    • Gluten-Free breadcrumbs
    A square pan of mac & cheese on a grey background
    An overhead shot of a pan of baked mac & cheese, surrounded by a few bowls of mac & cheese & salad

    Baked Mac and Cheese - Gluten-Free!

    KC Cornwell
    This gluten-free Baked Mac and Cheese is a crowd-pleasing favorite! Cheesy & creamy with a crunchy, buttery top, it's everything baked macaroni & cheese should be.
    5 from 1 vote
    Print Recipe Pin Recipe
    Prep Time 15 mins
    Cook Time 45 mins
    Course Main Course
    Cuisine American
    Servings 9 servings
    Calories 376 kcal

    Ingredients
      

    • ½ pound  Gluten Free elbow macaroni see notes
    • 3 tablespoon  butter
    • 3 tablespoon Gluten-Free Flour Blend or 2 tablespoons rice flour + 1 tablespoon tapioca starch
    • 1 ½ tablespoon powdered mustard
    • 3 cups milk
    • ½ cup yellow onion finely diced
    • 1 teaspoon paprika
    • 1 large egg
    • 12 oz sharp cheddar shredded
    • 1 ½ teaspoon kosher salt
    • Fresh black pepper

    Optional Topping:

    • 3 tablespoon butter
    • 1 cup Gluten Free panko breadcrumbs or 1 cup rough-chopped Gluten Free croutons or potato chips

    Instructions
     

    • Preheat oven to 350 degrees F. Butter a 2-quart casserole dish and set aside.
    • 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 ¾ of the cheese. Season with salt and pepper. Fold the cooked & drained macaroni into the mix and pour into a the casserole dish. Top with remaining cheese.

    Add the Topping:

    • Melt the butter in a sauté pan and toss the breadcrumbs to coat. Top the macaroni with the bread crumbs.

    Bake the Macaroni & Cheese:

    • Bake for 35-40 minutes. Remove from oven and rest for five minutes before serving.

    Video

    YouTube video

    Notes

    You can use elbow or penne pasta in this recipe.
    Serves 8-9 as a side dish, 4-6 as a main dish.
     
     
     

    Nutrition

    Calories: 376kcalCarbohydrates: 26gProtein: 15gFat: 24gSaturated Fat: 14gPolyunsaturated Fat: 1gMonounsaturated Fat: 6gTrans Fat: 0.3gCholesterol: 86mgSodium: 747mgPotassium: 178mgFiber: 1gSugar: 5gVitamin A: 880IUVitamin C: 1mgCalcium: 377mgIron: 1mg
    Keyword gluten-free pasta, mac and cheese, macaroni and cheese

    Photos: Meg van der Kruik

    Enjoy this gluten-free macaroni and cheese recipe? Check out these too!

    Bacon Pimento Macaroni and Cheese

    We are confident you will enjoy this Southern-inspired gluten-free bacon pimento macaroni and cheese recipe.

    It's ideal for a potluck, as a side dish, or combined with a fresh green salad for a satisfying meal.

    You'll want to prepare this dish repeatedly!

    You will never eat a better macaroni and cheese than this. Swear.

    Kimchi Mac and Cheese

    Get ready for a total mac and cheese game changer!!! This Kimchi mac and cheese is spicy, tangy, and creamy with a perfectly golden, crispy top. Each bite gets an extra flavor punch from a special mixture of fresh herbs.

    gluten free stovetop macaroni and cheese

    Gluten-Free Stove Top Macaroni and Cheese

    Stove top macaroni and cheese that the kids will absolutely love, and so rich and delicious that adults will love it, too? 

    Yeah, this one's a keeper...

    FAQs about Macaroni & Cheese:

    Why is my mac n cheese so soggy?

    Overcooking the pasta is usually the reason macaroni & cheese is soggy.
    Remember that the macaroni is cooked a second time whether you're making baked or stovetop mac and cheese. 
    You're guaranteed to have soggy macaroni after phase two of cooking if you cook pasta fully the first go-around.

    Why do you put eggs in mac n cheese?

    Adding an egg will make your mac and cheese smooth and creamy, and help baked macaroni to bind. 

    Should I cover my mac n cheese when baking in the oven?

    Most cooks prefer to bake their mac and cheese in an open oven, especially when topping it with breadcrumbs. A crusty top and corners form when baking without covering, creating a perfect contrast to the creamy dish.
    However, using a cover when baking macaroni and cheese is not in itself incorrect.

    Why is my mac n cheese sauce grainy? 

    Due to curdling, dairy sauces are prone to turning grainy or gritty. Macaroni and cheese sauce could also be grainy if the flour used to thicken cheese sauce isn't fully incorporated, or if nut meal or coarsely ground flour is used.

    Milk and fat are used to make cheese sauce. The proteins do tend to want to separate. Causes of graininess from dairy are typically excessive heat, lack of fat, or excessive acid. To prevent this, cook cheese sauce over medium heat and avoid nonfat or low fat products.

    Why is my mac n cheese oily?

    The fat in the cheese may separate if it is overheated or if the sauce is allowed to sit for a long time. To prevent this, cook cheese sauce over medium heat and combine with the pasta quickly after cooking.

    Can I freeze macaroni and cheese?

    That question comes up a lot, and I always respond "not really." 

    The pasta and cheese sauce will thicken as it sits, and the creamy texture simply vanishes when you defrost and bake, leaving it clumpy and thick. If you need to freeze macaroni and cheese before baking, add additional sauce.

     The Best Mac and Cheese Homemade Recipe

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    K.C. is a farm-grown foodie, born and raised in the fertile fields of California’s San Joaquin Valley. After being diagnosed with Celiac Disease following years of unexplained illness, she has infused her gluten-free life with flavor, fork in hand. Learn more about K.C.

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