This comforting Butternut Squash Mac and Cheese adds earthy butternut squash to the homemade sauce and melts perfectly into golden cheesy goodness. It’s a hearty dish you can pair it with a crisp salad for a warm, wholesome dinner.

Jump to:
- Why You Will Love This Butternut Squash Macaroni and Cheese Recipe
- Ingredients
- Variations
- How to Make Butternut Squash Mac and Cheese
- Storage Directions
- Serving Suggestions
- Expert Tips
- Try This Delicious Mac and Cheese With Butternut Squash Today
- More Delicious Pasta Recipes to Try
- Butternut Squash Macaroni and Cheese
If you love mac and cheese, I’ve got a winner for you today. This tasty mac and cheese is combined with butternut squash for a rich flavor blast and a dose of veggies in every bite.
This rich, cheesy dish has been a staple in my rotation for a while, now. I love it because it’s a fun twist on traditional mac and cheese, and it helps me get some vegetables into my grandchildren. This is one of my favorite dishes for dinner or potlucks. I’ve even been known to bring it to Thanksgiving dinners!
While making this dish might be simple, the flavor profile is rich and complex. It’s a delicious fall side that everyone always comes back for again and again.
If your house is a huge fan of mac and cheese you’ve got to try our classic mac and cheese recipe or this cheesy beef pasta!

Why You Will Love This Butternut Squash Macaroni and Cheese Recipe
- Healthier Option: This for sure is not a healthy dish! It’s mac and cheese! It’s simple carbs, butter, and cheese. However, it has a healthy twist with the addition of the butternut squash.
- Great Flavor: We know our macaroni and cheese so you can be sure it’s creamy and delicious!
- Solution for Picky Eaters. And if you struggle to get veggies into picky eaters this dish makes a great option! The twist of butternut squash adds some vitamins, minerals, and fiber not found in regular mac.
Ingredients
The ingredients for this recipe are very basic. You’ll most likely have most of them in your kitchen already. Any that you don’t have are easily found at your local grocery store.
- Shell pasta: I used shells in this recipe, but you can use any short noodle you like. Elbow macaroni, ziti, penne, and the like are all excellent choices.
- Butter and All purpose flour: The base of our cheese sauce. The flour is added to melted butter to make a roux.
- Milk: The creamy addition to make our sauce extra creamy. Use full fat milk for the best flavor and texture.
- Butternut squash: We start by roasting fresh butternut squash. If you wan tto save some time you can use canned butternut squash puree instead.
- Sharp cheddar cheese: We prefer the bold tangy flavor of sharp cheddar but really you can use any meltable cheese you love. Gouda is particularly good with the butternut squash.
- Seasoning: We like to add Slap Ya Mama for a bit of spice along with salt, black pepper, garlic powder, and onion powder.
Variations
The great thing about macaroni and cheese of any kind is how versatile it is, and this recipe is no different. You can easily make this recipe exactly as you want it by simply changing a few things to fit your tastes.
- Add Protein: Add some meat to turn this side into a main course. Add ground beef crumbles, shredded chicken, diced ham, cooked bacon, or even cooked ground turkey will work well.
- Add Veggies: Broccoli is a great choice, but you can feel free to experiment with any of your favorite veggies.
- Try Pumpkin Instead: You can easily make pumpkin mac and cheese by using pumpkin puree instead of the butternut squash.

How to Make Butternut Squash Mac and Cheese
Making this dish is as easy as shopping for it. Even though you’ll be roasting and pureeing the squash, it’s still an incredibly straightforward recipe. It only takes a few steps, and you’ll be all done! Gather all your ingredients, preheat oven to 350 degrees F, and line a baking sheet with parchment paper. Then you can get started!
- Step 1: Prep the Squash. Cut the squash in half lengthwise, scoop out the seeds, and brush both sides with olive oil. Place it cut side down on your prepared baking sheet.
- Step 2: Bake and Puree. Bake the squash for 1 hour or until tender. Scoop out the flesh and place it into a large bowl. Puree with a blender or food processor, or you can mash it with a hand masher until smooth.
- Step 3: Cook the Pasta. Cook the pasta in boiling water according to package directions. Drain and set aside.
- Step 4: Cook the Sauce. Melt the butter in a skillet over medium heat. Add the flour and whisk until combined. Pour half of the milk into the skillet and whisk until smooth. Next, add the remaining milk and whisk again. Stir in the butternut squash puree and then add the cheese and stir until it’s melted. Add your seasonings and mix one last time.
- Step 5: Put it Together. Add the pasta to the cheese sauce mixture. Stir well and serve it immediately. Enjoy!
Storage Directions
- Refrigerator: Store your leftover mac and cheese in the refrigerator in shallow, airtight containers for 3 – 5 days.
- Freezing: Mac and cheese freezes very well. Chill it completely in the refrigerator. Then, cut it into individual portions and double wrap them in cling wrap and then a singe layer of aluminum foil. Finally, place them in an airtight, freezer-safe container or heavy-duty freezer bags.
- Reheat: Use the microwave to heat up individual servings or you can reheat it in a skillet. I like to add a bit of milk when heating it up to help it regain some its creaminess.

Serving Suggestions
Enjoy your mac and cheese with butternut squash you just about any meat entree! It goes great with our thin chicken breasts or these slow cooker pork ribs.
Turn it into a vegetarian main dish and serve with our lemon pepper asparagus, some roasted broccoli or Brussels sprouts.
It makes a seasonal side dish for Thanksgiving too! We love it along with some Instant Pot mashed potatoes, sweet potato biscuits, and slow cooker chicken and stuffing!
Expert Tips
- Buy Block Cheese: You can use any variety but I highly recommend grating block cheese rather than buying pre-shredded cheese. You will end up with a creamier cheese sauce.
- Don’t Overcook the Pasta: Cook it just until al dente for the best texture!

Try This Delicious Mac and Cheese With Butternut Squash Today
This unique mac and cheese recipe is rich, creamy, and cheesy, with an added sweet earthiness that you can only get with the addition of butternut squash. It’s the perfect side for almost any main dish, especially during the fall when the squash is the freshest. It’s a flavor combo that everyone loves, and I think you will, too. Give this recipe a try. I know you’ll love it.
More Delicious Pasta Recipes to Try
If you are looking for more delicious butternut squash recipes, make sure to check out Ahead of Thyme’s blog. She has lots of delicious recipes you might enjoy as well.
If you try this recipe and love it, please be sure to leave a 5 โญ๏ธโญ๏ธโญ๏ธโญ๏ธโญ๏ธ rating below and comment! You can also pin it to save it for later. Also, you can follow us on Pinterest, Facebook, Instagram and YouTube. Remember to “like” or “follow” us on all social media.

Butternut Squash Macaroni and Cheese
Ingredients
- 16 ounce box small pasta shells
- 2 tablespoons butter
- 2 tablespoons all purpose flour
- 2 cups milk
- 1 ยฝ cups butternut squash puree
- 2 cups sharp cheddar cheese, shredded
- 1 teaspoon Slap Ya Mama
- ยฝ teaspoon salt
- ยฝ teaspoon pepper
- ยฝ teaspoon garlic powder
- ยฝ teaspoon onion powder
Instructions
- Preheat oven to 350ยฐ and line a baking sheet with parchment paper.
For the Butternut Squash Puree
- Cut squash lengthwise, scoop out the seeds, and brush both sides with olive oil. Place on prepared baking sheet.
- Bake for 1 hour or until tender. Scoop out flesh and place into large bowl. Puree or mash with a hand masher until smooth.
For the Mac and Cheese
- In a large pot over high heat, boil water, add pasta, and cook per package directions. Drain and set aside.
- In a large skillet over high heat, melt butter, add flour, and whisk until combine. Pour half of the milk into the skillet, whisk until smooth. Next, add the remaining milk. Stir to combine.
- Add butternut squash puree, stir, then add the cheese and stir until melted. Season with Slap Ya Mama, salt, pepper, garlic powder, and onion powder. Stir.
- Add pasta, stir and serve immediately. Enjoy!
Notes
- Buy Block Cheese: You can use any variety but I highly recommend grating block cheese rather than buying pre-shredded cheese. You will end up with a creamier cheese sauce.
- Don’t Overcook the Pasta: Cook it just until al dente for the best texture!











