Creamy, cozy and full of flavor. This baked butternut squash mac and cheese is an easy, wholesome twist on classic comfort food and it can easily be made gluten free. Make as side dish or as the star of the meal.
Love butternut squash? Then be sure to try my fall quinoa salad with butternut squash and maple Dijon sheet pan with salmon.
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"SUPER yummy! Nice change to a regular cheesy pasta dish that we often eat at our house! Kids don't even know they're eating squash!" - Gina
Reasons to Love This Recipe
- Sage and Nutmeg - Butternut squash pasta is not complete without sage, and I add just the right amount to the topping to compliment every bite. And just a touch of nutmeg adds flavor and depth to bring out the fall vibes.
- Cheesy, but not heavy - Because the butternut squash provides some creaminess, you don't need to go too heavy on the cheese, keeping this dish lighter than traditional baked mac and cheese.
- Make ahead friendly - This can easily be made ahead of time and baked when needed, making food prep for holidays a breeze! Try my cold wild rice salad recipe or easy savory sweet potato casserole for more make-head holiday side dishes.
- No roux needed - The butternut squash thickens the sauce nicely so no roux is needed (keeping it extra easy to make).
Baked butternut squash mac & cheese, anyone? You know you want some! I am mostly dairy-free, but every once in a while life calls for cheese and this is one of those times. Thanksgiving is coming up so you know I am going to splurge on the dairy.
The butternut squash gives this dish warm, cozy flavors and creaminess and a little bit of cheese keeps it nice and light and not overly rich... now that's my kind of mac and cheese!
Ingredient Notes
- Chicken bone broth - Using some broth instead of all milk really elevates the flavor with the butternut squash. I like bone broth for the nutrients and protein, but any chicken broth of vegetable broth can be used (just don't use beef broth).
- Whole milk - Whole milk is best, but even 2% can be used.
- Penne noodles - I'm a huge fan of penne in this baked butternut squash mac and cheese, but you could swap for any other tubular pasta, like ziti, rigatoni, or even fusilli (I just prefer noodles on the larger side).
- Sharp cheddar cheese - For the best flavor, be sure to use sharp white cheddar. Do NOT use pre-shredded cheese - it doesn't melt the same.
A complete list of ingredients can be found in the recipe card below. The above are some specific notes to help with selecting ingredients.
Substitutions & Variations
- Use gluten-free noodles for gluten-free baked butternut squash mac and cheese. All the other ingredients are naturally gluten free. Jovial makes the best noodles and I like using their gluten-free penne in this recipe. I also use their noodles in my skillet vegetarian lasagna.
- If looking to cut down on the dairy, you can use almond milk in place of the whole milk. I have tested this, and it turns out well - just be sure to melt the cheese with the milk at very low heat so the almond milk doesn't curdle. Use an almond milk with no fillers or gums.
- I love the simplicity of just using sharp cheddar cheese, but you could replace about ⅓ of the cheese with shredded gruyere. Gruyere is great in mac and cheese!
- Add in some pre-cooked chopped chicken and/or some sauteed broccoli, kale, or spinach to make it a complete meal.
How to Make Baked Butternut Squash Mac & Cheese
Step 1: Place cubed squash on baking sheet and toss with oil, salt, and pepper. Add garlic cloves.
Step 2: Bake at 400-degrees F for 20-25 minutes, or until squash is lightly browned and fork tender. While the squash is baking, cook noodles to el dente.
Step 3: Add the cooked squash, roasted garlic (skin removed), onion powder, nutmeg, salt, and broth to a high speed blender.
Step 4: Blend until smooth.
Step 5: To a large stock pot, add the milk and heat over medium-low heat. Stir in 12 oz of the shredded cheddar and mix until the cheese is fully melted. Turn off the heat and add the butternut squash puree - mix until combined
Step 6: Add the cooked noodles to the pot and mix until noodles are coated in the sauce.
Step 7: Transfer noodles to a baking dish and top with remaining shredded cheese and chopped fresh sage.
Step 8: Bake for 20-25 minutes at 350-degrees F, or until edges are bubbly.
Top tip: Broil for 3-5 minutes so the cheese topping gets extra crisp and bubbly.
Cutting Butternut Squash
It's much more cost effective to buy an actual squash and cut it yourself, however, around the holidays, you're sure to find it pre-cut in the produce section of your local grocery store. You can really use either, but I like buying the squash myself.
If you're new to cutting up a whole squash, follow these quick steps below:
- Start by cutting the ends from the butternut squash.
- Using a standard vegetable peeler or Y-shaped vegetable peeler, carefully peel the skin from the butternut squash. After the squash has been peeled, cut the squash in half lengthwise and scoop out the seeds.
- Place butternut squash cut side down on cutting board and cut into ½ inch slices. Cut the slices into about ½ inch cubes. Now you're cubed squash is ready for roasting!
Tips & Notes
For an extra-cheese-y baked butternut squash mac and cheese, layer some additional shredded cheese between the noodles before baking.
Be sure to use freshly grated cheese and NOT pre-shredded. Pre-shredded does not melt the same.
The pasta will continue to cook in the oven, so don't overcook the noodles. Al dente (firm to the bite, maybe still a slight crunch) is how they should be cooked.
Add an optional crumb topping by mixing 1 cup panko bread crumbs (gluten free if needed), 3 tbsp. of melted butter and a pinch of salt and sprinkling over the top before baking.
Throw in any extra roasted butternut squash cubes with the noodles before baking. The chunks of squash mixed in with the mac and cheese is amazing! Or use them in this kale and butternut squash salad.
Recipe FAQs
Yes! You can keep the prepped mac and cheese in the fridge and baked directly from the fridge. Just add an additional 10 minutes or so, as it will need slightly longer to warm up.
Absolutely! Either will work - just roast until tender before adding to the blender.
Storing
Leftovers should be stored in an airtight container in the fridge and will stay fresh for up to 5 days. Reheat in a microwave safe dish in the microwave until heated to your liking, or place back in the stove at 350 until heated through.
Tip: Add a splash of milk when reheating to keep it creamy.
Other Side Dishes I Think You'll Love
If you make this recipe, please let me know what you think! I would so appreciate you leaving a star rating and/or comment below. And don't forget to share a photo on Instagram or Facebook and mention @CleanPlateMama!
Eat Clean.Be Well!
-Sara
Baked Butternut Squash Mac and Cheese (gluten-free option)
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Equipment
- 1 Baking sheet
- 1 large stock pot
- 1 baking dish
Ingredients
- 4 cups butternut squash, peeled and cubed (about a 2lb squash)
- 2 tsp. extra-virgin olive oil or avocado oil
- 3 cloves garlic (4 if on the small side)
- 1 tsp. onion powder
- ¼ tsp. ground nutmeg
- ½ tsp. fine sea salt
- 1 cup chicken bone broth
- 16 oz penne noodles (gluten-free if needed)
- 1 ¾ cups whole milk
- 16 oz sharp white cheddar cheese, shredded and divided
- ⅓ cup chopped fresh sage
Instructions
- Preheat oven to 400-degrees F.
- Place cubed butternut squash on a baking sheet and drizzle with olive oil and season with salt and pepper. Mix squash with olive oil to evenly coat. Add garlic cloves (with paper skin ON) to the baking sheet. Bake squash and garlic for 20-25 minutes, or until squash is fork tender. Remove garlic from skin after it's roasted (you can easily squeeze the garlic from the skin once it's roasted).
- While the squash is roasting, using a large stock pot, cook the pasta to el dente (or even slightly under el dente as it will continue to cook when it's baked). Drain and set aside. Return stock pot to the stove as you'll use this to make the sauce.
- Once the squash is cooked, add the cooked squash, roasted garlic (skin removed), onion powder, nutmeg, salt, and broth to a high speed blender. Blend until smooth.
- To the large stock pot, add the milk and heat over medium-low heat. Stir in 12 oz of the shredded cheddar and mix until the cheese is fully melted. Turn off the heat and add the butternut squash puree - mix until combined. Taste sauce and adjust seasoning if you'd like (add more salt, pepper, nutmeg).
- Return the noodles back to the pot and mix noodles with sauce. Pour noodles into a 2-3 quart sized baking dish. Sprinkle with remaining 4 oz of cheese and the chopped sage.
- Bake for 20-25 minutes, or until edges are bubbly. Lastly, broil for 3-5 minutes to crisp up the top.
- Enjoy!
Notes
- Make sure to buy block cheese and shred the cheese yourself. Pre-shredded cheese doesn't melt as well.
- I prefer Penne noodles, but any tube shaped noodle will work. Use gluten-free noodles for gluten-free. I prefer brown rice noodles (GF) or whole wheat noodles.
- Chicken bone broth, chicken broth, or vegetable broth can be used (just don't use beef broth).
- If you have extra squash, throw the roasted squash cubes in with the noodles before baking. The chunks of squash with the mac and cheese is amazing!
Nutrition
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Sara says
Love the subtle flavor of the butternut squash and that fact that we are getting some veggies in with our mac and cheese. So good 🙂
Gina says
SUPER yummy! Nice change to a regular cheesy pasta dish that we often eat at our house! Kids don’t even know they’re eating squash!
Sara says
yay! I'm glad the kids can't tell they is some nutrition in it too!
Julie says
Made this to prep for Thanksgiving and had a little taste... it was so good! Looking forward to the final version! Thanks for the great recipe!
Sara says
So glad you liked it. Thanks so much!
Christine says
This looks amazing! Can't wait to try it!