If you’re looking for that perfect cozy-meets-healthy comfort dish, you can’t go wrong with this Baked Spaghetti Squash and Cheese Recipe. Imagine all the creamy, cheesy goodness of classic mac and cheese, but lightened up with tender, golden squash strands that twirl just like noodles! Whether you’re feeding your family, meal-prepping for busy weekdays, or celebrating veggie-forward eating, this dish delivers on both taste and nostalgia with every bubbling, golden forkful.

Baked Spaghetti Squash and Cheese Recipe - Recipe Image

Ingredients You’ll Need

This Baked Spaghetti Squash and Cheese Recipe keeps things delightfully simple with just a handful of real ingredients. Each one has a purpose—either bringing creaminess, adding a kick of flavor, or lending that beautiful, gooey texture we all crave in a baked casserole.

Spaghetti Squash: About 3 pounds, this squash magically transforms into golden, tender strands that mimic pasta while sneaking in extra veggies.
Olive Oil: Just a drizzle helps roast the squash to perfect tenderness and adds a mild fruity note.
Butter: For richness and to start the base of your velvety cheese sauce.
Garlic: Fresh cloves, minced, to infuse the sauce with savory depth.
All-Purpose Flour: Thickens the sauce and gives it that classic, creamy texture. (Almond flour is a good lower-carb option!)
Milk: The foundation of any great cheese sauce; whole, low-fat, or any milk of your choice works here.
Sharp Cheddar Cheese: Bold, melty, and the star of that gooey, cheesy pull.
Parmesan Cheese: A salty, nutty boost that rounds out all the flavors and helps brown the top.
Salt & Black Pepper: Enhances every bite—don’t skip them!
Ground Mustard (optional): Lends a little background tang that wakes up the cheese sauce.
Paprika: Adds gentle heat and that beautiful warm color to the crust.
Chopped Parsley (optional): Sprinkled on top for a fresh, vibrant garnish that finishes the dish.

How to Make Baked Spaghetti Squash and Cheese Recipe

Step 1: Roast the Spaghetti Squash

Preheat your oven to 400°F (200°C). Cut the spaghetti squash in half lengthwise, scoop out the seeds, and drizzle the cut sides with olive oil. Arrange the halves cut side down on a parchment-lined baking sheet. Roast for 35 to 40 minutes, or until the flesh is tender and easily shreds into spaghetti-like strands with a fork—it should just give when you press the outside.

Step 2: Prepare the Cheesy Sauce

While your squash roasts, melt butter in a medium saucepan over medium heat. Add the minced garlic and sauté just until fragrant—about 1 minute is all it takes for maximum flavor. Whisk in the flour and cook for another minute to gently toast it, making sure there are no lumps. Gradually add the milk, whisking constantly. Keep stirring for about 3 to 4 minutes until the sauce thickens a bit and coats the back of a spoon.

Step 3: Add the Cheeses and Seasoning

Take the saucepan off the heat and add your shredded cheddar, grated Parmesan, salt, pepper, ground mustard (if using), and paprika. Stir it all together until the cheese melts into a silky, luscious sauce. This is where the magic (and the aroma!) really starts to happen.

Step 4: Combine Squash and Cheese Sauce

Once the squash is cool enough to handle, use a fork to gently scrape the flesh into strands. Tumble them into a large bowl, then pour that dreamy cheese sauce right over the top. Give everything a sweet and thorough mix so every strand is cloaked in cheesy goodness.

Step 5: Bake Until Golden and Bubbly

Spoon the mixture into a greased 8×8-inch baking dish and smooth the top. Pop it into a 375°F (190°C) oven for 15 to 20 minutes. You’re looking for a bubbling, golden top that signals crispy edges and melty, irresistible cheese. Sprinkle with chopped parsley for a final burst of color and freshness.

How to Serve Baked Spaghetti Squash and Cheese Recipe

Garnishes

This Baked Spaghetti Squash and Cheese Recipe loves a finishing flourish! A handful of fresh chopped parsley gives it a bright look and herby lift. You could also try a dusting of extra Parmesan or a light sprinkle of crushed red pepper flakes if you want to add a bit of zing.

Side Dishes

Pair this dish with something crisp and green, like a lemony arugula salad or simple roasted asparagus, to balance out the luscious cheesiness. Warm garlic bread or a crusty baguette is also a perfect match if you want to soak up every last drop of sauce.

Creative Ways to Present

For a fun twist, serve the cheesy squash right in its roasted shell for a playful, eye-catching presentation. Alternatively, scoop individual portions into ramekins for a dinner-party feel, or top with a sprinkle of crispy bacon bits or sautéed spinach to switch up the flavor and add extra flair.

Make Ahead and Storage

Storing Leftovers

Any leftovers from your Baked Spaghetti Squash and Cheese Recipe can be stored in an airtight container in the refrigerator for up to 3 days. The flavors mingle and get even more delicious over time, so you might find yourself sneaking an extra spoonful straight from the fridge!

Freezing

If you want to save some for later, cool the bake completely and portion it into freezer-safe containers. It will keep well for up to 2 months. When ready to enjoy, just thaw overnight in the fridge for the best texture and taste.

Reheating

To reheat, cover and bake leftovers at 350°F (175°C) for about 20 minutes, or rewarm individual servings in the microwave until hot. Add a splash of milk or a sprinkle of cheese if needed to freshen up the sauce and bring back some creaminess.

FAQs

Can I make this Baked Spaghetti Squash and Cheese Recipe fully ahead of time?

Absolutely! Prepare the squash and cheese sauce, assemble in your baking dish, cover, and refrigerate for up to 24 hours. Simply bake when you’re ready to serve, adding a few extra minutes to heat through.

Is this recipe gluten-free?

As written, it includes all-purpose flour, but swap in a gluten-free flour blend or almond flour, or simply leave it out for a thinner sauce so the Baked Spaghetti Squash and Cheese Recipe stays gluten-free and just as tasty.

What can I add if I want to boost protein or veggies?

Diced cooked chicken, crumbled bacon, sautéed spinach, or steamed broccoli fold beautifully into the cheese-squash mixture before baking, making this dish heartier and even more colorful.

How do I know when the spaghetti squash is perfectly roasted?

The squash is ready when the flesh is golden, tender, and you can pull it into noodle-like strands with a fork—all with no resistance. If the strands seem tough, simply pop it back in for another 5–10 minutes.

Can I use a different cheese for this recipe?

Certainly! Although sharp cheddar is the classic, a blend of Gruyere, fontina, Monterey Jack, or even a little pepper jack can add different flavors and textures to your Baked Spaghetti Squash and Cheese Recipe.

Final Thoughts

I genuinely hope you’ll give this Baked Spaghetti Squash and Cheese Recipe a place at your table. It’s a feel-good, crowd-pleasing way to eat your veggies and satisfy that comfort food craving in every warm, bubbly bite. Enjoy every gooey forkful—you deserve it!

Baked Spaghetti Squash and Cheese Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

4.8 from 28 reviews

Author: admin
Total Time: 1 hour 10 minutes
Yield: 4 servings 1x
Diet: Gluten-Free (with flour substitute), Vegetarian

Print Recipe

Description

Indulge in the comforting flavors of this Baked Spaghetti Squash and Cheese recipe. A healthier twist on traditional mac and cheese, this dish features roasted spaghetti squash coated in a creamy, cheesy sauce for a satisfying meal.

Ingredients

Scale

Spaghetti Squash:

1 medium spaghetti squash (about 3 pounds)
1 tablespoon olive oil

Cheese Sauce:

2 tablespoons butter
2 cloves garlic (minced)
2 tablespoons all-purpose flour
1 ½ cups milk
1 cup shredded sharp cheddar cheese
1/2 cup grated Parmesan cheese
1/2 teaspoon salt
1/4 teaspoon black pepper
1/4 teaspoon ground mustard (optional)
1/4 teaspoon paprika
1 tablespoon chopped parsley (optional, for garnish)

Cook Mode Prevent your screen from going dark

Instructions

Preheat the oven: Preheat the oven to 400°F (200°C).
Prepare the squash: Cut the spaghetti squash in half lengthwise, remove the seeds, drizzle with olive oil, and roast cut side down on a baking sheet for 35-40 minutes.
Make the cheese sauce: Melt butter, sauté garlic, add flour, whisk in milk, then add cheddar, Parmesan, salt, pepper, mustard, and paprika until smooth.
Combine: Scrape the cooked squash into strands, mix with cheese sauce, transfer to a baking dish.
Bake: Bake at 375°F (190°C) for 15-20 minutes until bubbly.
Serve: Garnish with parsley and enjoy!

Notes

Add cooked bacon, sautéed spinach, or broccoli for extra flavor and nutrition.
For a lower-carb sauce, replace flour with almond flour or omit it for a thinner cheese sauce.

Prep Time: 15 minutes
Cook Time: 55 minutes
Category: Main Course
Method: Baking
Cuisine: American