If you’ve been searching for a comforting dish that’s both wholesome and bursting with flavor, you’re about to fall in love with this Baked Spaghetti Squash and Cheese Recipe. It takes the naturally sweet, tender strands of spaghetti squash and wraps them in a creamy, cheesy sauce with fresh spinach and a crispy golden Parmesan topping. This recipe is a perfect blend of nutrition and indulgence, making it a brilliant way to enjoy vegetables in an utterly satisfying way. Plus, it’s great for family dinners or when you want to impress friends with a meal that looks and tastes like you spent hours in the kitchen, but is surprisingly straightforward to make.

Ingredients You’ll Need
The magic of this Baked Spaghetti Squash and Cheese Recipe lies in its simple yet carefully chosen ingredients. Each element contributes something special—texture from the squash, creaminess from the cheese sauce, and vibrant color and nutrition from the spinach. You’ll be amazed how these humble ingredients come together to create something so delicious.
- 5 ½ cups cooked spaghetti squash: The star of the dish, providing a mild, slightly sweet base that mimics pasta strands perfectly.
- ¼ cup minced onion: Adds a gentle sharpness and depth to the creamy sauce.
- 4 cups baby spinach: Brings freshness, color, and a boost of leafy greens to balance the richness.
- 1 tablespoon butter: Used to create a luscious roux that thickens the cheese sauce.
- 1 tablespoon olive oil: Enhances flavor and helps sauté the onions until tender and fragrant.
- ¼ cup flour: The thickening agent for a smooth, velvety sauce; gluten-free flour works beautifully here if needed.
- 2 cups skim milk: Keeps the sauce creamy yet light, so it doesn’t overpower the squash.
- 1 cup fat-free chicken broth: Adds savory notes and depth, or vegetable broth for a vegetarian option.
- Salt and pepper to taste: Essential for bringing out all the flavors in perfect harmony.
- â…› cup grated Parmesan cheese: Sprinkled on top for that signature golden crust and a punch of umami.
- 2 cups (8 oz) reduced-fat mild cheddar cheese: Melts into the sauce creating a rich, gooey texture that makes this recipe irresistible.
How to Make Baked Spaghetti Squash and Cheese Recipe
Step 1: Cook the Spaghetti Squash
Start by preheating your oven to 375°F. Cut the spaghetti squash in half lengthwise and scoop out the seeds—you’ll want to wear an apron for this part because it can be a bit messy! Place the squash halves cut-side down on a baking sheet and roast for about an hour until the flesh is tender enough to shred with a fork. Once cooked, use a fork to scrape out the squash strands and gently squeeze out any excess liquid. This step is key to avoid a watery final dish.
Step 2: Create the Cheese Sauce
While the squash roasts, melt the butter together with olive oil in a saucepan over medium heat. Toss in the minced onions and let them soften for a couple of minutes—you’ll know they’re ready when they turn translucent and fragrant. Stir in the flour and cook, stirring constantly for 3 to 4 minutes to form a roux. Gradually whisk in the skim milk and chicken broth, bringing the mixture to a boil. Then reduce the heat and let it simmer until thick and creamy, about 2 minutes. Season with salt and pepper to taste. This smooth cheese sauce is the secret to the irresistible creaminess of the dish.
Step 3: Combine Ingredients
Remove the sauce from heat and stir in the shredded cheddar cheese until melted and smooth. Then, fold in the cooked spaghetti squash strands and fresh baby spinach. The spinach wilts slightly from the warmth, adding a lovely vibrant green color and freshness that balances the richness beautifully.
Step 4: Bake to Perfection
Transfer the cheesy spaghetti squash mixture into a baking dish and sprinkle evenly with grated Parmesan cheese on top. Bake at 375°F for 25-30 minutes, or until the top turns bubbly and golden brown. This finishing touch adds a crispy, savory crust that elevates every bite.
How to Serve Baked Spaghetti Squash and Cheese Recipe

Garnishes
A sprinkle of freshly chopped parsley or basil adds a pop of color and a subtle herbal aroma that brightens the dish. For a bit of heat and extra flavor, try a light dusting of smoked paprika or chili flakes right before serving. These garnishes take your Baked Spaghetti Squash and Cheese Recipe from delicious to show-stopping.
Side Dishes
This dish pairs wonderfully with a crisp green salad tossed in a tangy vinaigrette to contrast the creamy texture. Roasted or steamed vegetables like asparagus or Brussels sprouts add another layer of flavor and nutrients. For a heartier meal, serve alongside grilled chicken or a light fish for protein-rich balance.
Creative Ways to Present
For a casual gathering, serve the baked spaghetti squash cheesy goodness straight from a rustic ceramic baking dish. Impress dinner guests by portioning it into individual ramekins topped with a Parmesan crisp or fresh microgreens. You can even hollow out a freshly baked mini spaghetti squash and fill it with this cheesy mixture for a charming edible bowl!
Make Ahead and Storage
Storing Leftovers
Leftover Baked Spaghetti Squash and Cheese Recipe keeps wonderfully in an airtight container in the refrigerator for up to 4 days. The flavors deepen as it rests, making for easy, tasty leftovers that reheat well during busy weekdays.
Freezing
This recipe freezes beautifully, making it ideal for meal prep. After baking and cooling completely, portion into freezer-safe containers or bags. It can be frozen for up to 3 months. When ready to enjoy, thaw overnight in the fridge before reheating.
Reheating
For best results, reheat leftovers covered with foil in a 350°F oven until heated through, about 20 minutes. You can also microwave individual portions, stirring halfway to ensure even warmth. Add a quick sprinkle of extra cheese or fresh herbs before serving for a fresh touch.
FAQs
Can I substitute the cheddar cheese with another type?
Absolutely! While mild cheddar offers a great balance of flavor and meltability, feel free to use mozzarella, monterey jack, or even gouda. Just make sure the cheese melts well to maintain that creamy texture.
Is this recipe gluten-free?
It can be! Simply swap the all-purpose flour with a gluten-free flour blend in the cheese sauce step to keep this Baked Spaghetti Squash and Cheese Recipe completely gluten-free without sacrificing taste or texture.
Can I make this recipe vegetarian?
Yes, you can easily make it vegetarian by using vegetable broth instead of chicken broth. The rest of the ingredients are already vegetarian-friendly, making this dish suitable for many diets.
How do I know when the spaghetti squash is fully cooked?
The flesh should be tender enough to shred easily with a fork and have a slightly translucent appearance. If it feels hard or resistant when scraping, it needs a bit more roasting time.
Can I add other vegetables to the recipe?
Definitely! Feel free to mix in mushrooms, roasted red peppers, or sun-dried tomatoes when combining the cooked squash with the cheese sauce. These additions add exciting flavors and textures that complement the core dish beautifully.
Final Thoughts
I can’t recommend enough trying this Baked Spaghetti Squash and Cheese Recipe for your next cozy dinner. It’s a perfect balance of comfort and healthfulness wrapped in creamy, cheesy goodness that everyone will love. Whether you’re cooking for family or friends, this dish is sure to become a favorite in your recipe collection. Enjoy every bite!
Print
Baked Spaghetti Squash and Cheese Recipe
- Prep Time: 15 minutes
- Cook Time: 1 hour 30 minutes
- Total Time: 1 hour 45 minutes
- Yield: 7 servings
- Category: Main Course
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
This Baked Spaghetti Squash and Cheese recipe is a comforting, lighter alternative to traditional pasta casseroles, featuring tender roasted spaghetti squash strands combined with fresh spinach and a creamy, cheesy sauce made from reduced-fat cheddar and Parmesan. Baked to golden perfection, it delivers a satisfying, wholesome meal perfect for family dinners or meal prep.
Ingredients
Spaghetti Squash
- 5 ½ cups cooked spaghetti squash (from about 2 small spaghetti squashes)
Vegetables and Aromatics
- ¼ cup minced onion
- 4 cups baby spinach
Cheese Sauce
- 1 tablespoon butter
- 1 tablespoon olive oil
- ¼ cup all-purpose flour (use gluten-free flour for GF)
- 2 cups skim milk
- 1 cup fat-free chicken broth (substitute 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 the oven to 375°F. Cut the spaghetti squash in half lengthwise and remove the seeds. Place each half cut-side down on a baking sheet and bake for about 1 hour, or until the flesh is tender and easily separates into strands when scraped with a fork. Once cooked, use a fork to scrape out the squash strands and gently squeeze out any excess liquid.
- Make Cheese Sauce: In a medium saucepan, melt the butter and olive oil together over medium heat. Add the minced onions and sauté for about 2 minutes until softened. Stir in the flour and cook the mixture, stirring constantly for 3-4 minutes to form a roux. Gradually whisk in the skim milk and fat-free chicken broth, bringing the mixture to a boil. Then reduce the heat and simmer for about 2 minutes until the sauce thickens. Season with salt and pepper to taste.
- Combine Ingredients: Remove the cheese sauce from heat and stir in the reduced-fat cheddar cheese until it melts completely. Add the cooked spaghetti squash strands and fresh baby spinach into the sauce and stir to combine evenly.
- Bake: Pour the mixture into a baking dish and sprinkle the grated Parmesan cheese evenly on top. Bake in the preheated oven for 25-30 minutes or until the dish is bubbly and the top is golden brown.
Notes
- To make this dish vegetarian, substitute the chicken broth with vegetable broth.
- For a gluten-free version, use gluten-free flour instead of all-purpose flour.
- To reduce the sodium content, use low-sodium broth and adjust salt to taste.
- Spinach can be substituted with kale or Swiss chard for a different flavor and texture.
- Leftovers can be refrigerated for up to 3 days and reheated in the oven or microwave.

