If you’re looking for a comforting dish that combines the natural sweetness of roasted squash with the rich creaminess of cheese, this Baked Spaghetti Squash and Cheese Recipe is an absolute must-try. This recipe turns humble spaghetti squash into a cheesy, satisfying casserole that’s both wholesome and delicious. Perfect as a hearty main or a delightful side, it’s a dish that proves eating vegetables can be indulgent and satisfying at the same time.

Ingredients You’ll Need
The ingredients for this Baked Spaghetti Squash and Cheese Recipe are wonderfully straightforward yet essential for building its luscious texture and vibrant flavor. Each one plays a special role—whether it’s the nuttiness of Parmesan, the brightness of spinach, or the creamy sauce that brings everything together flawlessly.
- 5 ½ cups cooked spaghetti squash: This is the star, providing a tender, stringy base that mimics pasta perfectly.
- ¼ cup minced onion: Adds subtle sweetness and aromatic depth.
- 4 cups baby spinach: Brings a fresh, slightly earthy crunch and vibrant green color.
- 1 tablespoon butter: Essential for a silky, rich cheese sauce foundation.
- 1 tablespoon olive oil: Enhances flavor and helps sauté the onions nicely.
- ¼ cup flour: Acts as the thickening agent for the creamy cheese sauce; gluten-free flour works great too.
- 2 cups skim milk: Keeps the cheese sauce smooth and lighter without losing creaminess.
- 1 cup fat-free chicken broth: Adds savory flavor and balances the richness (use vegetable broth to keep it vegetarian).
- Salt and pepper: Season to taste for the perfect burst of flavor.
- â…› cup grated Parmesan cheese: Adds a nutty, salty finish on top when baked.
- 2 cups mild cheddar cheese (2% reduced-fat): Melts beautifully into the sauce, delivering that classic cheesy goodness.
How to Make Baked Spaghetti Squash and Cheese Recipe
Step 1: Cook Spaghetti Squash
Start by preheating your oven to 375°F. Cut two small spaghetti squashes in half lengthwise and scoop out the seeds. Place them cut-side down on a baking sheet and bake for about one hour until the flesh is tender and can easily be shredded with a fork. Once baked, scrape out the strands carefully, then squeeze out any excess moisture – this step ensures your casserole won’t be watery.
Step 2: Make the Cheese Sauce
While your squash is baking, melt the butter and olive oil together in a saucepan over medium heat. Add minced onions and cook until soft, about two minutes. Then stir in the flour and cook for another 3-4 minutes, stirring constantly. Gradually whisk in the milk and chicken broth, bringing the sauce to a gentle boil before reducing the heat to let it thicken for about 2 minutes. Don’t forget to season with salt and pepper, which makes the flavors pop.
Step 3: Combine Ingredients
Remove the sauce from heat and stir in the cheddar cheese until it melts completely, creating a velvety, rich cheese sauce. Fold in the cooked spaghetti squash strands and fresh baby spinach, which wilts down beautifully in the residual heat, adding a lovely touch of color and nutrition.
Step 4: Bake to Perfection
Pour the cheesy spaghetti squash mixture into a greased baking dish and sprinkle the top with grated Parmesan cheese. Bake in the preheated oven for 25-30 minutes or until the dish is bubbly and the top has turned a gorgeous golden brown. This final step melds all the flavors together and creates that irresistible crust on top we all love.
How to Serve Baked Spaghetti Squash and Cheese Recipe

Garnishes
The Baked Spaghetti Squash and Cheese Recipe is wonderful as is, but a sprinkle of freshly chopped parsley or basil adds a burst of fresh color and herbaceous brightness that balances the richness. A dash of crushed red pepper flakes can also bring a little pleasant heat to the dish.
Side Dishes
This cheesy bake pairs beautifully with lighter sides to round out your meal. Consider serving it alongside a crisp mixed green salad with a tangy vinaigrette or some roasted Brussels sprouts. For a heartier meal, garlic bread or a crusty baguette complements the creamy texture perfectly.
Creative Ways to Present
For a fun twist, try serving the Baked Spaghetti Squash and Cheese Recipe in individual ramekins or hollowed-out spaghetti squash shells for a rustic, elegant presentation. You can also sprinkle toasted breadcrumbs on top before baking for extra crunch or mix in some cooked mushrooms or sun-dried tomatoes to personalize the flavors.
Make Ahead and Storage
Storing Leftovers
Store any leftover Baked Spaghetti Squash and Cheese in an airtight container in the refrigerator for up to four days. Covering it well helps maintain the creamy texture while keeping it fresh and ready for a quick reheat.
Freezing
This recipe freezes well if you want to prep ahead. Portion it into freezer-safe containers and freeze for up to two months. Thaw overnight in the fridge before reheating to retain its smooth, cheesy consistency without becoming watery.
Reheating
Reheat leftovers gently in the oven at 350°F until warmed through, which helps maintain the dish’s texture and prevents the cheese from separating. Microwave reheating works in a pinch but stir occasionally for even warmth and to avoid drying out the top layer.
FAQs
Can I use a different type of cheese?
Absolutely! While mild cheddar creates that classic cheesy flavor, you can experiment with mozzarella, Gruyère, or a sharp white cheddar for variations. Just choose cheeses that melt well to keep that creamy texture.
Is this recipe gluten-free?
It can be! Simply swap the all-purpose flour for a gluten-free flour blend of your choice when making the cheese sauce. This substitution keeps the dish just as creamy and delicious.
How do I know when the spaghetti squash is done baking?
When the flesh is fork-tender and easily separates into strands, your spaghetti squash is perfectly cooked. It should feel soft to the touch when you press the outer shell gently.
Can I make this recipe vegetarian?
Yes, replace the chicken broth with vegetable broth to keep the dish vegetarian-friendly while maintaining all the savory flavor you love. The cheese sauce will still be rich and satisfying.
What variations can I add to the recipe?
This recipe is a great canvas for added flavors—think cooked bacon or sausage for meat lovers, sautéed mushrooms for earthiness, or sun-dried tomatoes for a tangy pop. You can also mix in herbs like thyme or oregano to elevate the taste.
Final Thoughts
This Baked Spaghetti Squash and Cheese Recipe truly is a comforting crowd-pleaser that brings together healthful ingredients and indulgent flavors in one beautiful dish. Whether you’re enjoying it on a cozy night in or serving guests, it’s sure to become a new favorite. Give it a try and discover how delicious and satisfying wholesome cooking can be!
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Baked Spaghetti Squash and Cheese Recipe
- Prep Time: 15 minutes
- Cook Time: 1 hour 45 minutes
- Total Time: 2 hours
- Yield: 7 servings
- Category: Main Course
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
This Baked Spaghetti Squash and Cheese recipe is a comforting, nutritious twist on traditional cheesy pasta dishes. Using tender roasted spaghetti squash strands combined with a creamy, homemade cheese sauce and fresh spinach, this meal provides a delicious low-fat alternative that’s perfect for a family dinner or meal prep. Baked to perfection with a golden Parmesan crust, it’s a delightful combination of creamy, cheesy flavors with the light texture of roasted squash.
Ingredients
Spaghetti Squash
- 5 ½ cups cooked spaghetti squash (from about 2 small spaghetti squash)
Vegetables
- ¼ cup minced onion
- 4 cups baby spinach
Cheese Sauce
- 1 tablespoon butter
- 1 tablespoon olive oil
- ¼ cup flour (use gluten-free flour for gluten-free option)
- 2 cups skim milk
- 1 cup fat-free chicken broth (vegetable broth for vegetarian)
- Salt and pepper to taste
- â…› cup grated Parmesan cheese
- 2 cups (8 oz) Sargento 2% reduced-fat mild cheddar cheese
Instructions
- Cook Spaghetti Squash: Preheat your oven to 375°F (190°C). Cut the spaghetti squash in half lengthwise and carefully remove the seeds with a spoon. Place the squash halves cut-side down on a baking sheet lined with parchment paper or foil. Bake for about 1 hour, or until the squash is tender when pierced with a fork.
- Prepare Squash Strands: Once baked, use a fork to scrape the flesh of the squash into strands resembling spaghetti. Drain and squeeze out any excess liquid to prevent sogginess in the dish.
- Make Cheese Sauce: In a medium saucepan over medium heat, melt the butter together with the olive oil. Add the minced onions and cook for about 2 minutes until translucent. Stir in the flour and cook, stirring constantly, for 3 to 4 minutes to form a roux.
- Add Liquids and Thicken: Gradually whisk in the skim milk and fat-free chicken broth (or vegetable broth if vegetarian). Bring the mixture to a boil, then reduce heat and let it simmer for about 2 minutes until thickened. Season with salt and pepper to taste.
- Combine Cheese and Vegetables: Remove the saucepan from heat and stir in the mild cheddar cheese until fully melted and smooth. Fold in the spaghetti squash strands and baby spinach to evenly incorporate them into the sauce.
- Assemble and Bake: Pour the cheese and squash mixture into a greased baking dish. Sprinkle the grated Parmesan cheese evenly on top. Bake at 375°F (190°C) for about 25 to 30 minutes, or until the casserole is bubbly and the top is golden brown.
Notes
- For a gluten-free version, substitute flour with gluten-free flour or cornstarch.
- Use vegetable broth instead of chicken broth to make the dish vegetarian-friendly.
- To reduce sodium, use low-sodium broth and adjust salt to taste.
- Squeezing excess liquid from spaghetti squash is crucial to prevent watery casserole.
- Fresh spinach can be substituted with frozen spinach, but be sure to thaw and drain it well before adding.
- This dish reheats well and can be stored in an airtight container in the fridge for up to 3 days.

