Creamy Butternut Squash Mac and Cheese

This Creamy Baked Butternut Squash Mac and Cheese is a rich and comforting twist on the classic mac and cheese. With roasted butternut squash, sharp cheddar, and Gruyère cheese, it’s the ultimate cozy meal for fall. The crunchy top is made from pecan and breadcrumbs for a textural contrast. 

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Creamy Baked Butternut Squash Mac and Cheese

You know it’s officially cozy season when your morning walk includes frost instead of dew. The chilly season is here and I am ready for it, I’ve pulled out all my chunky sweaters, grabbed my apples for the season and went squash shopping the other day. If the morning is chill means cozy casseroles, pastas, stews and soups, I am here for it! I love summer but Fall so far has been an absolute stunner and the colder weather has me ready to bake, simmer and slow cook my way into winter.

This Creamy Baked Butternut Squash Mac and Cheese is the perfect dish to make this weekend! I love mac and cheese and I mean, I’m not sure I know a single soul alive who doesn’t. I grew up on Kraft Dinner like any 70’s kid, it was the goto when mom was working. We would add hotdogs into it if we were feeling fancy, and felt like we were eating like kings. My taste has um.. changed slightly and I haven’t had boxed mac and cheese or hotdogs in well over a decade; I’ll be honest, I am okay with that! What hasn’t changed is my love of mac and cheese; the ooey gooey, piping hot and wonderfully decadent type of mac and cheese that’s served at a buffet or family gathering.

Maybe growing up with mac and cheese is what makes it feel like the quintessential comfort food and this version is no exception. We’re taking the classic dish you know and love and giving it a delicious fall twist with creamy roasted butternut squash. I used a combination of sharp white cheddar and Gruyère, which melts beautifully into the sauce, giving you that luscious, creamy consistency. As you know, my mister is celiac so this dish is 100% gluten-free from noodles to topping and there was no skipping on flavour. 

Butternut Squash Mac and Cheese Ingredients

  • Butternut Squash: The star of the show! Cubed butternut squash adds a natural sweetness and creaminess when pureed, making it the perfect base for the cheese sauce.
  • Olive Oil & Butter: These add richness and help sauté the onion and garlic, as well as create a velvety cheese sauce.
  • Onion & Garlic: Essential aromatics for building flavour in the cheese sauce.
  • Gluten-Free Flour: Helps thicken the sauce without the gluten. Feel free to use regular flour if you’re not gluten-sensitive.
  • White Cheddar & Gruyère: The ultimate cheese combo. Sharp cheddar brings that classic mac and cheese flavour, while Gruyère adds a creamy, slightly nutty taste.
  • Milk & Chicken Stock: These liquids create the perfect base for a rich, creamy cheese sauce. You can easily swap the chicken stock for veggie stock to keep it vegetarian.
  • Cayenne Pepper & Nutmeg: These spices give the dish a subtle warmth and depth of flavour without overpowering the cheese or squash.
  • Gluten-Free Pasta: Any short pasta will work, but I prefer gluten-free to make this dish celiac-friendly. Use your favourite pasta, just be sure it’s cooked al dente as it will be baked afterwards.

Topping Ingredients

  • Raw Pecans: Add a crunchy, nutty element to the breadcrumb topping.
  • Gluten-Free Breadcrumbs: Give the mac and cheese that perfect golden crust. If I don’t have homemade gluten free breadcrumbs, this is the brand I love.
  • Sage: Adds an earthy, herbal flavour that pairs beautifully with the butternut squash.

How to Prepare the Butternut Squash for Mac and Cheese

To prep the butternut squash, peel it with a vegetable peeler and then cut into 1-inch cube pieces. Boil the cubes in salted water until they are tender. Puree the tender butternut squash in a food processor or blender until smooth.

How to Make Butternut Squash Mac and Cheese

Cook the Pasta

Preheat your oven to 400F and boil your gluten-free pasta until al dente. Reserve some pasta water for later, then drain and set aside.

Make the Cheese Sauce

Sauté the onion and garlic in olive oil and butter over medium heat. Add gluten-free flour, then whisk in milk and chicken stock to create a smooth sauce. Stir in white cheddar, Gruyère, and the squash puree, allowing everything to melt together into creamy goodness.

Combine & Bake

Stir the cooked pasta into the cheese sauce, then transfer it to an oven-safe dish. Top with extra cheese and the pecan breadcrumb topping.

Bake & Broil

Bake the mac and cheese at 400°F for 20 minutes, then broil for 3-5 minutes to get that golden, crispy topping.

How to Serve This Creamy Butternut Squash Mac and Cheese

This dish is hearty enough to stand alone as a meatless main dish for a holiday gathering or potluck, but it also pairs wonderfully with a light salad or roasted vegetables for a balanced meal. Serve it hot from the oven with a sprinkle of freshly ground black pepper and a side of crusty gluten-free bread to soak up any extra cheese sauce.

Why You’ll Love Butternut Squash Mac and Cheese

This dish is comfort food at its finest, with a fall twist thanks to the creamy roasted butternut squash. The combination of sharp cheddar and Gruyère cheese creates a rich, indulgent sauce that’s melt-in-your-mouth good. The fact that this recipe is gluten free makes it enjoyable for everyone and can easily be adapted to be vegetarian with the swap of stock. The pecan breadcrumb topping adds the perfect crunch, bringing everything together beautifully.

Butternut Squash Mac and Cheese Frequently Asked Questions

What else can I use the cheese sauce for? This butternut squash cheese sauce is incredibly versatile! Use it to top veggies, mix into baked casseroles, or drizzle over roasted potatoes for an extra cheesy side dish.

What does butternut mac and cheese taste like? The flavor is rich and creamy just like a traditional mac and cheese but has a hint of sweetness from the butternut squash.

How to reheat butternut squash mac and cheese? Reheat your mac and cheese in a 350°F oven for 15-20 minutes, or until heated through. You can also reheat individual portions in the microwave, but I recommend adding a splash of milk to keep it creamy.

Can you freeze butternut squash mac and cheese? Yes! You can freeze this mac and cheese before baking. Just prepare the dish, cover it tightly, and freeze for up to 3 months. When ready to bake, thaw overnight in the fridge and follow the baking instructions.

Is butternut squash mac and cheese healthy? While mac and cheese is traditionally indulgent, the addition of butternut squash adds a boost of fibre, vitamins, and antioxidants, making it a more nutrient-dense version of the classic dish. There are many ways that you can make this recipe more healthy like using high-protein pasta or adding vegetables.

Did you try this recipe? Leave a comment and review below!

Try these recipes next:

Butternut Squash Risotto

Roasted Garlic Carrot Squash Soup

Mustard Marinated Pork Chops With Cherry Mustard Sauce

TERI ANN CARTY

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Butternut Squash Mac and Cheese

This Creamy Baked Butternut Squash Mac and Cheese is a rich and comforting twist on the classic mac and cheese. With roasted butternut squash, sharp cheddar, and Gruyère cheese, it’s the ultimate cozy meal for fall. The crunchy top is made from pecan and breadcrumbs for a textural contrast.
5 from 1 vote
Print Pin Rate
Servings: 4
Author: Teri-Ann Carty
Prep Time: 30 minutes
Cook Time: 30 minutes
Total Time: 1 hour

Equipment

  • oven, stovetop, casserole dish or oven-safe deep sided pan

Ingredients

Mac and Cheese Ingredients

  • 340 gram short noodle of choice
  • 4 cups butternut squash cubed
  • 2 tbsp olive oil
  • 4 tbsp butter
  • pinch chili flakes
  • ½ onion diced
  • 2 garlic cloves minced
  • 2 tbsp gluten-free flour
  • 1 cup white cheddar shredded
  • 1 cup Gruyère shredded
  • 1 cup milk of choice I used unsweetened soy as it’s what I had
  • 1 cup chicken stock veggie stock works too
  • ½ tsp cayenne pepper
  • fresh nutmeg
  • sea salt and cracked pepper

Topping Ingredients

  • ½ cup raw pecans
  • ½ cup gluten free bread crumbs
  • 2-3 tbsp sage minced
  • 1 tbsp butter

Instructions

Topping Instructions

  • Melt butter in a pan over medium heat. Add breadcrumbs, pecans and sage. Mix together and cook until pecans start to smell toasty and sage is fragrant. Set aside.

Mac and Cheese Instructions

  • Preheat oven to 400 degrees.
  • Place squash in a pot and cover with water. Bring to a boil and cook until fork tender. Drain and place in a food processor. Process the squash until a puree is formed. Scrape into a container and cover with a lid.
  • Cook pasta until al dente. Reserve 1/2 cup of pasta water. Drain and set aside.
  • While pasta is cooking heat a large oven-safe pan over medium-high heat. Add olive oil, butter, chili flakes and onion. Cook until onion starts to soften and then add garlic and cook until fragrant.
  • Sprinkle flour over onion and garlic. Cook for one minute to cook off the raw flour.
  • Pour in chicken stock and milk. Whisk until the sauce is smooth.
  • Add cayenne pepper and freshly grated nutmeg, and whisk to combine.
  • Turn the heat up to allow the mixture to come to a bubble whisking constantly. Once sauce has thickened reduce heat to low and add squash puree.
  • Add cooked pasta and stir to thoroughly combine.
  • Add 1 cup of white cheddar and 1 cup of gruyere and stir to combine.
  • Sprinkle remaining cheddar on top and evenly spread crumb topping on top of the cheese.
  • Cover pan with a lid or tinfoil and place in the oven to bake for 20 minutes.
  • Increase the temperature to broil.
  • Remove lid and broil for 3-5 minutes until the topping is toasty and pasta is bubbly.
  • Allow it to cool for a minimum of 5 minutes before serving.

Notes

You don't need to use gluten-free flour or pasta if you don't want to! Use your favourite noodle but a short noodle is best!
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Nutrition

Serving: 1g | Calories: 680kcal | Carbohydrates: 37g | Protein: 21g | Fat: 52g | Saturated Fat: 22g | Polyunsaturated Fat: 6g | Monounsaturated Fat: 19g | Trans Fat: 1g | Cholesterol: 96mg | Sodium: 604mg | Potassium: 781mg | Fiber: 6g | Sugar: 7g | Vitamin A: 16230IU | Vitamin C: 36mg | Calcium: 592mg | Iron: 2mg

*Macros are provided as an estimate for convenience. Your final numbers will vary depending on ingredient brands, substitutions, and how you portion the recipe.

2 Responses

  1. 5 stars
    I made this with regular pasta and dairy products for a neighborhood pot luck. Honestly it was the BEST Mac ‘n cheese I’ve ever made. I did roast the cubed squash rather than boil it, puréed the cooked squash and added it to the bechamel. Everyone raved about it. Our hostess asked to keep the leftovers.

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