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Bacon Butternut Squash Mac and Cheese Casserole

This hearty Butternut Squash Mac and Cheese gives off all the comfort food vibes with its cheesy casserole goodness. It's topped with fried sage and a crispy pretzel breadcrumb topping.

Casserole dish with macaroni, cheese, bacon and herbs.

It's Fall, and what better way to officially ring it in than with a piping hot dish of cheesy, baked macaroni and cheese. With a twist.

This mac and cheese casserole incorporates butternut squash, bacon, sage and a pretzel breadcrumb topping.

Why Make Homemade Mac and Cheese with Butternut Squash

A fantastic way to get more veggies in your diet

Kids love this butternut mac just as much as traditional mac and cheese

This is hearty enough that it could be a main course on its own, but easy enough to be a side dish

It's relatively fast and ready in an hour and it's easy to customize for picky eaters


Get more info on all of these basic ingredients with the full recipe in the recipe card at the bottom of the post. 

  • Butternut squash- you want a smaller one, about 1 ½ pounds in weight
  • dry elbow macaroni, you could also use cavatappi if desired
  • bacon- sliced into one-inch strips
  • butter- unsalted is preferred since we salt later
  • sage leaves
  • chicken stock- choose low sodium if you have it. You could trade this out for vegetable broth if needed.
  • milk
  • flour- I use all purpose
  • sharp cheddar cheese- Freshly shredded cheese melts better than pre-shredded cheese
  • cream cheese- adds a nice creamy factor to your creamy sauce
  • pretzels- adds a nice crunch
  • salt and black pepper


First, bake the squash. Cut in half length wise and scoop out the seeds.

Drizzle with olive oil, and sprinkle liberally with salt and pepper.

Bake in a 400 degrees Fahrenheit oven for 45-60 minutes or until fork tender.

Roasted squash on a baking sheet.

Remove from the oven and allow to cool enough to handle. Scoop out the soft flesh and set aside.

Dice bacon into 1 inch pieces, and fry in a skillet until crispy. Drain on paper towels and set aside.

Boil the macaroni in salted water until two minutes under al dente. The pasta will finish cooking in the casserole.

Drain the pasta and rinse it with cold water in the strainer until cold.

Macaroni pasta in a pot with a cheesy sauce poured on.

Medium to sharp cheddar cheese is perfect for this recipe, but you can also try a blend of other cheeses.

Be sure to shred the cheese by hand off the block, and not use pre-shredded cheese because it won't melt smoothly.

In the same pot that you boiled the pasta in, sauté the sage leaves in butter until fried and crispy, remove with tongs and set aside.

Add the flour to the remaining butter and whisk to create a thickened paste, called a roux.

Add the stock and simmer until it becomes thickened and the flour taste is no longer detectable, about 5 minutes.

Lower the heat, then add the milk.

Add the baked butternut squash to the milk and stock mixture.

Use an immersion blender (or add contents to a regular blender) and blend on medium speed until smooth.

Add the shredded cheese and cream cheese and whisk until smooth.

Put the pretzels in a plastic bag.

Using a rolling pin, crush the pretzels and roll to pulverize them until they resemble crumbs.

Scoop being taken from a bacon mac and cheese casserole.

Add the cooked macaroni and bacon to butternut squash cheese sauce.

Pour it into a 13x9 inch (or similar sized) casserole dish.

Top with the fried sage leaves, followed by the pretzel breadcrumbs.

Put the baking dish in the oven and bake for approximately 20 minutes in a 425 degree Fahrenheit oven, until edges brown and the cheese is hot and bubbly.

Remove from oven, and serve hot.


Leftover Butternut Mac and Cheese can be stored in the refrigerator for up to 3 days. Place the mac and cheese in an airtight container before storing it in the fridge. 

To reheat, remove from fridge, and place portions in a shallow dish with a lid or cover with foil. Bake covered at 350 degrees Fahrenheit until heated through, about 25-30 minutes. Enjoy! 

What to serve with mac and cheese

Butternut mac and cheese can be served with a variety of sides. To complement the creamy cheese sauce, try pairing it with a light salad, roasted vegetables, or some steamed broccoli and green beans.

For a heartier dish, try serving it alongside some grilled chicken or steak. If you’re looking for something more indulgent, serve up a side of garlic bread or toasted ciabatta.

With its rich flavor and creamy texture, butternut mac and cheese is sure to be a hit at any dinner table.

Can I add more veggies? 

Sure, if you think you'd like extra veggies in this mac and cheese, try adding some mushrooms, broccoli, bell peppers, or even some sauteed spinach. Adding any of these veggies is a great way to bulk this out a little more. 

Can I use frozen butternut squash? 

I have not personally tested this recipe with frozen cut up butternut, but I did some research and have seen people use it successfully.

It is a time saver, so if that's something you want to try, feel free to do so and let me know how it goes in the comments below. 

You'll need to cook it according to the package instructions and then add it to the immersion blender as you did before. 

What other cheese varieties can I try? 

While I love the classic cheddar cheese recipe that brings the best flavor, you can definitely change it up or use a combination of cheese choices.

I think this would be good with white cheddar and you could sprinkle some parmesan cheese when you go to bake it. Whatever cheese you choose, I'm sure it will have a yummy, cheesy flavor. 

Do I have to use crushed pretzels?

If you would like to trade this out, you could try some breadcrumbs or panko bread crumbs instead of the pretzels. 

Recipe Tips

  • When cooking the pasta, check the package directions to see what your specific brand recommends.
  • You can bring even more fantastic flavor to this casserole by adding some spices like garlic powder or onion powder.
  • Using the pot with the pasta water to fry the sage leaves in helps make clean up time easier.
  • if your cheese sauce is too thick when reheating, you can add a splash of milk to help thin it out a little bit. 
  • You can use a food processor to crush the pretzels if you don't have a rolling pin.
  • Related recipes...

If you tried this recipe, let others know in the comments, or leave a rating in the recipe card.

📖 Recipe

Casserole dish with butternut squash macaroni and cheese spoonful being taken.

Bacon Butternut Squash Mac and Cheese

Elbow macaroni pasta, crispy bacon, and fried sage in a creamy butternut squash an cheddar cheese sauce, topped with crunchy pretzel breadcrumbs.
5 from 1 vote
Print Pin Rate
Course: dinner, Main Course
Cuisine: American
Keyword: bacon butternut squash mac and cheese, butternut squash cheese sauce
Prep Time: 30 minutes
Cook Time: 30 minutes
Servings: 12
Calories: 508kcal
Author: Erin
Cost: $5.95


  • 1 squash about 1 ½ pounds in weight
  • 1 lb elbow macaroni about 4 cups dry
  • ½ lb bacon sliced into one inch strips
  • 3 tablespoon butter plus more for squash
  • 5-10 sage leaves
  • 1 ½ cups chicken stock
  • 1 ½ cup milk
  • 2 tbsp flour
  • 2 cups sharp cheddar cheese or other melting cheese
  • 4 oz cream cheese
  • 1 cup pretzels crushed
  • salt and pepper to taste


  • Preheat oven to 400 degrees Fahrenheit.
  • Cut squash in half, longways and scoop out seeds.
  • Drizzle squash halves with olive oil and sprinkle with salt and pepper. Bake for 45-60 minutes, or until fork tender. Set aside to cooled enough to handle.
  • Boil pasta in salted water until two minutes short of al dente, according to pasta package instructions, drain and rinse with cold water. Set aside.
  • Fry bacon until crispy, drain on paper towels and set aside.
  • Crush pretzels in a plastic zip lock bag using a rolling pin until they resemble breadcrumbs.
  • In the same pot that the pasta was boiled in fry the sage leaves in butter on medium high heat until fried and crispy, remove the leaves.
  • Add flour to the butter that the sage was fried in and whisk until thick paste, or roux, has formed.
  • Pour in chicken stock, whisk, and simmer until thickened and flour taste is no longer present, about 5 minutes.
  • Reduce heat to low and stir in the milk.
  • Scoop the soft, cooked flesh out of the roasted squash and add to the pot of stock mixture.
  • Use an immersion blender, or transfer to a blender or food processor and blend/pulse on medium speed until smooth.
  • Fold in the shredded cheese and cream cheese and stir on low heat until smooth.
  • Salt and pepper to taste.
  • Fold in the cooked macaroni pasta and bacon.
  • Pour into a 13x9 inch, or similarly sized casserole dish.
  • Top with fried sage and crushed pretzel breadcrumbs.
  • Bake for 20-30 minutes until golden brown.


  • It's advised to use dry pasta, and only cook it a couple of minutes below al dente. 
  • If you use a combination of gruyere with the cheddar, or other smooth melting cheese, you may not need to use all of the cream cheese, or possibly omit it all together.  
  • Cook the bacon as crispy as possible without burning it, so that it doesn't become soggy in the butternut squash mac and cheese casserole. 


Calories: 508kcal | Carbohydrates: 45g | Protein: 13g | Fat: 31g | Saturated Fat: 14g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 12g | Cholesterol: 52mg | Sodium: 325mg | Potassium: 423mg | Fiber: 3g | Sugar: 5g | Vitamin A: 7016IU | Vitamin C: 13mg | Calcium: 224mg | Iron: 2mg
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