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The Best Gluten-Free Mac and Cheese!

by Capri Lilly

Creamy Homemade Mac and Cheese with savory butternut squash, a blend of four cheeses, simple spices, and gluten-free noodles! This dish is surely one that your family will love!

If you’re looking for a dish to pair with this Mac & Cheese, try my Red-Wine Braised Short Ribs or Herb-Crusted Spatchcock Chicken recipe!

creamy gluten-free mac and cheese

Mac and cheese is a staple at any Thanksgiving dinner, holiday party, or family gathering. And not just any mac and cheese! It has to be creamy, flavorful, and oozing with cheese. Definitely nothing out of a box with powdered cheese or pre-made; only the old-fashioned traditional way!

Today I am going to share my most requested recipe, and undeniably everyone’s favorite: The Best Creamy Homemade Mac and Cheese, completely Gluten-Free!

southern mac and cheese

How To Make The Best Gluten-free Mac and Cheese

The secret to making the best mac and cheese is to use a variety of cheeses! Block Cheese is best, but if you’re not up to shredding the cheese yourself, pre-shredded cheese works just as well. I use both!

In this recipe I use shredded sharp cheddar cheese, a shredded cheese blend of Parmesan, Asiago, Fontina, & Mild Provolone cheese, and a block of Gruyere Cheese. 

cheddar cheese for mac and cheese

To avoid gluten in this recipe, I use Trader Joe’s Gluten Free Penne Noodles, which cooks nicely! These noodles are the perfect texture and don’t take away from the flavor of the mac and cheese.

As always, when making your own mac and cheese at home, feel free to use whichever noodles (gluten-free or regular)  and cheese you prefer!

Gluten-Free Macaroni Noodles

Here are a few good options (that I have tried and like): 

Barilla Gluten Free Elbow Pasta

Banza Chickpea Elbow Pasta

For this recipe I use penne noodles: Trader Joe’s Organic Brown Rice Penne Pasta

gluten free cheese sauce without flour

Gluten-Free Cheese Sauce Without Flour

The first step to making incredible mac and cheese is to make a cheese sauce. The cheese sauce is what coats all of the noodles (to make sure your mac and cheese is not dry once it’s done) and provides a rich flavor! The cheese sauce is typically made with a roux, which is essentially butter and flour, along with buttermilk, cheese, and seasonings. 

To keep this dish gluten-free, I use almond flour to make the roux. The almond flour works perfectly and does not effect the taste of the cheese sauce. 

My favorite almond flour to use is Blue Diamond Almond Flour

creamy macaroni and cheese with butternut squash

Butternut Squash Mac and Cheese

The secret to the creaminess of my mac and cheese:  it’s the butternut squash!

The butternut squash does not have a strong taste and honestly you wouldn’t know it was in the recipe unless I told you. Yet, it makes all the difference in the creaminess and enhanced flavor of this macaroni and cheese dish! All I will say is don’t knock it until you try it! You’ll be surprised how much you’ll enjoy this recipe and it is a great way to add vegetables and healthy nutrients to your favorite soul-food dish.

I recently learned that while growing up my parents had been adding shaved carrots to our mac and cheese for years! I had NO IDEA! Their mac and cheese was, and still is, always my favorite!

Adding veggies to this dish is the perfect way to make your dish a little healthier and give the kids veggies in a stealthy way that they will love!

Creamy Homemade Mac and Cheese (Gluten-Free)

I hope you enjoy this Creamy Gluten-Free Homemade Mac and CheeseIf you try the recipe, don’t forget to rate the recipe and let me know what you think in the comments below! Take pictures, tag #goodfoodbaddie, and share it with me on Instagram! I love hearing from you!

southern mac and cheese
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5 from 1 vote

Gluten-Free Mac and Cheese

Creamy Homemade Mac and Cheese with savory butternut squash, a blend of four kinds of cheese, simple spices, and gluten-free noodles! This dish will surely one that you’re family will love!
Prep Time15 mins
Cook Time30 mins
Total Time45 mins
Course: Dinner, Main Course, Side Dish
Cuisine: American, Gluten-Free
Keyword: cheese, creamy, gluten-free, good food baddie, goodfoodbaddie, mac and cheese, macaroni, pasta, southern
Servings: 10
Calories: 606kcal
Author: Capri Lilly


  • 16 oz Gluten-Free Pasta (or regular pasta)
  • 4-5 cups water
  • 1.5 cups Butternut Squash
  • 2 cups Shredded Cheese Blend (I used Trader Joes- Parmesan, Asiago, Fontina, & Mild Provolone Cheese)
  • 2.5 cups Shredded Sharp Cheddar Cheese
  • 8 oz Gruyere Cheese, cut into cubes
  • 2 cups Heavy Whipping Cream
  • 2 tbsp Butter
  • 2 tbsp Almond Flour (or any regular or alternative flour)
  • 1 tsp Italian Seasoning
  • 1 tsp Dried Oregano
  • 1 tsp Paprika
  • 3 Garlic Cloves, minced
  • Salt and Pepper, to taste


  • Preheat the oven to 350°F
  • In a large pot, add water and ¼ tsp of salt. Bring the water to a boil. Pour the pasta noodles into the boiling water and reduce to medium-low heat. Cook the pasta until al dente.
  • Season the butternut squash with salt, pepper, and 1 tbsp of Olive oil. Roast the butternut squash in the oven for 25-30 minutes. Once the squash is fully roasted, place the squash in a blender and blend for 1-2 minutes. (feel free to use 1-2 tbsp of the Heavy Whipping cream to make the butternut squash puree smoother)
  • In a medium saucepan, melt butter over medium-low heat. (You do not want the butter to burn because the flavor will come up in the sauce). Stir in 2 tbsp Almond Flour (or any regular/alternative flour). Continuously stir to make a roux.
  • Slowly pour in the 2 cups of Heavy Whipping Cream into the roux, stirring continuously. Stir in the Italian Seasoning, Paprika, Oregano, Salt, Pepper, and minced Garlic.
  • Add the butternut squash puree and stir until it is blended in and the sauce is smooth and clump-free.
  • Reduce to low heat and add stir the shredded cheeses into the sauce. Continue to stir until the cheese is melted and the sauce has slightly thickened.
  • Put the noodles into a large casserole dish, pour the sauce over the noodles, and mix well.
  • Top the mac and cheese with any remaining shredded cheese and add any cubed cheese into the dish.
  • Bake at 375°, with the first 20 minutes covered with foil and the last 10 minutes uncovered (to get the perfect golden crust).



  • If you are not sensitive to gluten, you can use regular all-purpose flour and regular elbow noodles. 
  • When the pasta is cooked to al dente, drain and rinse the pasta in cold water to stop the pasta from cooking any further.
  • You can use pre-cut butternut squash (12 ounces) or roast a medium-sized butternut squash. If you are roasting a whole squash, cut the squash in half lengthwise and roast flesh side up for 35 minutes, or until the inside is soft. 
  • Store any leftovers in an airtight container. You can reheat the mac and cheese in the oven or microwave.

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More Gluten-Free Side Dishes

Vegan Mashed Potatoes picture
Vegan Garlic Mashed Potatoes
roasted Brussels sprouts with butternut squash and bacon
Roasted Butternut Squash
pasta salad recipe
Mediterranean Pasta Salad

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Britney Brown November 18, 2020 - 8:52 pm

5 stars
The addition of the butternut squash made this recipe soooo creamy! Also, the cheese used here really complimented each other so well!

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