Butternut Squash Mac and Cheese
Butternut squash mac and cheese starts with a smooth squash puree stirred into a classic cheese sauce. You get a velvety, mildly sweet sauce that clings to every noodle. It works as a weeknight main or a fall side, and I share my tips below.

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Why This Butternut Squash Mac and Cheese Recipe Works
This mac and cheese tastes like a classic cheese sauce, with squash adding body and mild sweetness. Some popular versions cook everything in one pot or simmer the squash in broth. Mine keeps each step separate, so you control the thickness of the sauce.
The key is steaming the squash until it is very soft, about 10 to 12 minutes. Soft squash blends smoothly, and smooth squash gives you a silky sauce with no lumps. I cook the butter and flour paste for one to two minutes so the sauce never tastes floury.
Love cooking with squash? Try my simple butternut squash casserole, carrot and butternut squash soup, or creamy butternut squash pasta sauce.
Ingredients

- Elbow macaroni: The small tubes catch the sauce, and small shells work the same way.
- Butternut squash: Steamed and blended, it gives the sauce body and a mild, natural sweetness.
- Butter: It forms the base of the sauce and adds richness.
- All-purpose flour: Cooked with the butter, it thickens the milk into a smooth sauce.
- Milk: Whole or 2% milk keeps the sauce creamy without making it heavy.
- Sharp cheddar cheese: It brings the bold cheese flavor that balances the sweet squash.
- Mozzarella cheese: It melts smoothly and gives the sauce a gentle stretch.
- Parmesan cheese: It adds a salty, savory bite to every spoonful.
- Salt and black pepper: They season the sauce so the squash and cheese taste balanced.
- Garlic powder and onion powder: They add savory depth with no chopping.
- Nutmeg: A small pinch is optional, but it brings out the squash flavor.
- Reserved pasta water: The starchy water thins the sauce without dulling the flavor.
How To Make Butternut Squash Macaroni and Cheese

- Melt the butter in a large saucepan over medium heat. Cook the macaroni in salted water until just al dente. Reserve 1/3 cup of the pasta water, then drain.

- Whisk in the flour until it forms a paste. Cook it for 1 to 2 minutes, until lightly golden.

- Slowly whisk in the milk. Stir constantly for 4 to 5 minutes, until the sauce thickens.

- Steam or boil the cubed squash for 10 to 12 minutes, until very soft. Blend it until completely smooth, using a blender or an immersion blender.

- Stir the squash puree into the milk sauce until it looks smooth and golden.

- Stir in the salt, black pepper, garlic powder, onion powder, and nutmeg, if using.

- Reduce the heat to low. Stir in the cheddar, mozzarella, and Parmesan until fully melted and smooth.

- Add a splash of the reserved pasta water if the sauce is too thick. Stir until it looks glossy.

- Add the cooked pasta to the sauce.

- Fold until every noodle is evenly coated. Serve warm.
Tips for Butternut Squash Macaroni and Cheese
- Buy pre-cubed squash. It saves the peeling and cutting, and it steams just like fresh squash.
- Shred your own cheese. Freshly shredded cheese melts smoother than the bagged kind.
- Save the pasta water. Add it a splash at a time until the sauce looks glossy and pourable.
- Use an immersion blender. You can puree the squash right in its pot and skip an extra dish.
- Prep the squash ahead. Steam and blend it a day early, then refrigerate it until dinner.

Common Mistakes to Avoid When Making Butternut Squash Macaroni and Cheese
- Overcooking the pasta. It keeps softening in the hot sauce, so drain it just past al dente.
- Undercooking the squash. Firm pieces will not blend smoothly and leave the sauce gritty.
- Adding the milk too fast. Pour it in slowly while whisking so the flour paste does not clump.
- Melting the cheese over high heat. Keep the burner on low so the sauce stays smooth instead of oily.
- Skipping the flour paste. Cook it until lightly golden, or the sauce can taste raw and floury.
FAQ for Butternut Squash Mac and Cheese
Do you have questions about this recipe? Here are the answers to the most commonly asked questions.
It tastes mostly like cheese, with a mild sweetness from the squash. Sharp cheddar and Parmesan keep the flavor bold.
Yes. Thaw the cubes and drain them well. Then steam until very soft and blend as directed.
Yes. Roast the cubes until very soft, then blend them smooth. Roasted squash is drier, so you may need extra pasta water.
Yes. Make the sauce up to a day ahead and refrigerate it. Rewarm it over low heat with a splash of milk before folding in the pasta.
Pork pairs well with the sweet squash. Try my lemon pepper pork chops, bourbon glazed pork chops, or dutch oven pork tenderloin. A green salad or roasted green beans also round out the plate.

How to Store and Reheat
- Storage: Refrigerate leftovers in an airtight container for up to four days.
- Freezing: Freeze cooled mac and cheese in a freezer-safe container for up to two months. Thaw it overnight in the refrigerator.
- Reheating: Warm it on the stove over low heat with a splash of milk, stirring often. Single servings also reheat in the microwave in 30-second bursts.

Butternut Squash Mac and Cheese
Equipment
- large pot
- colander
- steamer basket
- Blender or immersion blender
- large saucepan
- whisk
Ingredients
- 12 ounces elbow macaroni or small pasta shells
- 2 cups peeled butternut squash cubed
- 2 tablespoons butter
- 2 tablespoons all-purpose flour
- 2 cups milk whole or 2%
- 1 cup sharp cheddar cheese shredded
- ½ cup mozzarella cheese shredded
- ¼ cup grated Parmesan cheese
- ½ teaspoon salt
- ¼ teaspoon black pepper
- ¼ teaspoon garlic powder
- ¼ teaspoon onion powder
- 1 pinch nutmeg optional
- â…“ cup reserved pasta water as needed for thinning
Instructions
- Bring a large pot of salted water to a boil. Cook the macaroni until just al dente.
- Reserve 1/3 cup of the pasta water, then drain the pasta and set it aside.
- Steam or boil the butternut squash for 10 to 12 minutes, until very soft.
- Blend the squash until completely smooth, using a blender or an immersion blender.
- Melt the butter in a large saucepan over medium heat. Whisk in the flour and cook for 1 to 2 minutes, until lightly golden.
- Slowly whisk in the milk. Stir constantly for 4 to 5 minutes, until the sauce thickens.
- Stir in the squash puree, salt, black pepper, garlic powder, onion powder, and nutmeg, if using.
- Reduce the heat to low. Stir in the cheddar, mozzarella, and Parmesan until fully melted and smooth. Add a splash of the reserved pasta water if the sauce is too thick.
- Fold in the cooked pasta until evenly coated. Serve warm.
Disclaimer:
Any nutritional data I provide is an approximation and actual dietary information can vary based on ingredients and proportion sizes.
