Cheesy Baked Spaghetti Squash with Marinara Sauce
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This cheesy spaghetti squash casserole is vegetarian comfort food.
Spaghetti squash is a gift from the diet gods. When roasted, it miraculously transforms into low-carb, low-cal, spaghetti-like strands. Here, I toss it with good-quality jarred marinara sauce, top it with shredded cheese and crispy bread crumbs, and bake it until gooey and golden brown. The casserole makes a comforting vegetarian main course or side dish for meatballs or Italian sausage.
If you’ve never cooked spaghetti squash, it can be a little intimidating because it’s one of those large, awkward vegetables you’re not quite sure how to go at. For this recipe, I use two medium squash rather than one large one, as the smaller squash are easier to cut. I also sharpen my chef’s knife before I get started; it makes all the difference. (Pro tip: you’re much more likely to cut yourself with a dull knife than a sharp one. I use an electric knife sharpener regularly to keep my knives in tip-top shape.)
What You’ll Need To Make Cheesy Baked Spaghetti Squash
Step-by-Step Instructions
Step 1: Prep the Spaghetti Squash
Using a very sharp chef’s knife, cut a sliver off of the stem end of each squash (this creates a flat surface to cut the squash in half). 
Stand each squash upright on a cutting board and slice through them top to bottom to cut each squash in half (use your body weight to press the knife down).
Using a soup spoon, scrape out the seeds and discard them.
Step 2: Roast the Spaghetti Squash
Place the squash halves cut-side-up on a foil-lined baking sheet. Drizzle with the oil and sprinkle evenly with 1 teaspoon salt and 1/2 teaspoon pepper.
Flip the squash halves so they are cut-side-down.
Roast for 40 to 50 minutes, or until the squash is golden brown underneath and the flesh is tender when pierced with a fork. You should be able to scrape the strands away from the skin easily. Flip the squash halves so they are cut-side-up, and let sit until cool enough to handle.
Use a fork to scrape out and fluff the strands.
Step 3: Toss the Spaghetti Squash with Sauce and Seasonings
Increase the oven temperature to 425°F. Place the strands in a large bowl. Add the marinara sauce, 3/4 teaspoon salt, 1/4 teaspoon pepper, and thyme.
Toss gently until the squash is evenly coated. Taste and add adjust seasoning if necessary.
Step 4: Assemble and Bake
Transfer the mixture to a 9 x 13-inch baking dish.
Sprinkle the mozzarella cheese evenly over top, followed by the Parmigiano-Reggiano.
In a small bowl, combine the melted butter with the panko, and mix until the panko is evenly coated.
Sprinkle the panko mixture evenly over the cheese.
Bake for 25 to 30 minutes, or until the top is golden.
Let cool for a few minutes, then sprinkle with more fresh thyme and serve.
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Cheesy Baked Spaghetti Squash with Marinara Sauce
This cheesy spaghetti squash casserole is vegetarian comfort food.
Ingredients
- 2 medium spaghetti squash (about 2½ pounds each)
- 1 tablespoon extra-virgin olive oil
- Salt
- Freshly ground black pepper
- 1¾ cups jarred marinara sauce, best quality such as Rao's or Victoria
- 2 teaspoons chopped fresh thyme, plus more for serving (or ¾ teaspoon dried)
- 1½ cups shredded whole milk mozzarella cheese
- 3 tablespoons finely grated Parmigiano-Reggiano
- 1½ tablespoons unsalted butter, melted
- ¾ cup panko bread crumbs
Instructions
- Preheat the oven to 400°F and set an oven rack in the middle position. Line a baking sheet with heavy-duty aluminum foil for easy clean-up.
- Using a very sharp chef's knife, cut a sliver off of the stem end of each squash (this creates a flat surface to cut the squash in half). Stand each squash upright on a cutting board and slice through them top to bottom to cut each squash in half (use your body weight to press the knife down).
- Using a soup spoon, scrape out the seeds and discard them.
- Place the squash halves cut-side-up on the prepared baking sheet. Drizzle with the oil and sprinkle evenly with 1 teaspoon salt and ½ teaspoon pepper. Flip the squash halves so they are cut-side-down. Roast for 40 to 50 minutes, or until the squash is golden brown underneath and tender when pierced with a fork. You should be able to scrape the strands away from the skin easily. Flip the squash halves so they are cut-side-up, and let sit until cool enough to handle. Use a fork to scrape out and fluff the strands.
- Increase the oven temperature to 425°F.
- Place the strands in a large bowl. Add the marinara sauce, ¾ teaspoon salt, ¼ teaspoon pepper, and thyme and toss gently until the squash is evenly coated. Taste and add adjust seasoning if necessary. Transfer the mixture to an ungreased 9 x 13-inch baking dish. Sprinkle the mozzarella cheese evenly over top, followed by the Parmigiano-Reggiano.
- In a small bowl, combine the melted butter with the panko, and mix until the panko is evenly coated. Sprinkle the panko mixture evenly over the cheese. Bake for 25 to 30 minutes, or until the top is golden. Let cool for a few minutes, then sprinkle with more fresh thyme and serve.
- Make-Ahead/Freezer-Friendly Instructions: The casserole can be assembled and refrigerated for up to 2 days before baking, or frozen for up to 3 months. Bake directly from the refrigerator or freezer, allowing a few extra minutes in the oven.
Pair with
Nutrition Information
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- Per serving (6 servings)
- Calories: 452
- Fat: 26 g
- Saturated fat: 14 g
- Carbohydrates: 39 g
- Sugar: 16 g
- Fiber: 7 g
- Protein: 20 g
- Sodium: 1,252 mg
- Cholesterol: 70 mg
This website is written and produced for informational purposes only. I am not a certified nutritionist and the nutritional data on this site has not been evaluated or approved by a nutritionist or the Food and Drug Administration. Nutritional information is offered as a courtesy and should not be construed as a guarantee. The data is calculated through an online nutritional calculator, Edamam.com. Although I do my best to provide accurate nutritional information, these figures should be considered estimates only. Varying factors such as product types or brands purchased, natural fluctuations in fresh produce, and the way ingredients are processed change the effective nutritional information in any given recipe. Furthermore, different online calculators provide different results depending on their own nutrition fact sources and algorithms. To obtain the most accurate nutritional information in a given recipe, you should calculate the nutritional information with the actual ingredients used in your recipe, using your preferred nutrition calculator.
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Much to my surprise this was really delicious. Spaghetti squash is often so blah and the ingredient list didn’t give any clue as to how good this would be. Healthy and light; we both loved it. I even had some cold for breakfast! Wonderful addition to the weekly routine and a good way to introduce this often forgotten vegetable to our meals. Thanks Jen. I should never have doubted you!!
Love this recipe and am making it all the time. It’s just the two of us, so I either cut it in half using an 8 x 8 or save and reheat a little later in the week depending on the squash that are available.
Couple of things I found that made the prep easier (and less scary!). Once you trim the stem end off, and stand the squash up– cut down one side through the middle then turn the squash 180 degrees and run the knife through the other side rather than trying to split the whole thing with one cut. It makes use of the hollow center and you need much less force. I then use an ice cream scoop to remove the seeds more efficiently. Makes this a pleasure to prepare and eat!
Thank you for pointing out the easier slicing technique – useful for arthritic hands. We just purchased both of Jenn’s books (as a thank you to her for the many, many recipes of hers we’ve enjoyed over the years).
I was very happy to find this recipe as my compost pile gave me a large amount of “volunteer” squash and I was looking for a new way to serve them. I recently read somewhere to cut the squash across the equator; it really makes a big difference in obtaining long strands of squash. thanks for all you do…I love your recipes!
I was pleasantly surprised by this recipe! Until I made this, I haven’t loved spaghetti squash, but I do enjoy most recipes from this site so decided to give it a try and am very glad I did as it was very flavorful prepared in this way. My husband liked it too!
This recipe sounds divine! I’m wondering how cooked shrimp would taste with this since I have some to use up.
Sure, Terry, that should work. Please LMK how it turns out!
This recipe was so good and great for a healthy, quick weeknight meal!
My husband and I absolutely loved this! I served it with Jenn’s Turkey, Spinach and Cheese Meatballs and it was a big hit. Lots of leftovers for lunches too. Thanks for the great recipe!
So delicious—I used gluten free bread-crumbs–but otherwise made just as Jenn’s wonderful recipe specifies. This was so good my family asked me to make again two days later!
I’m trying to implement meatless Mondays. This will be perfect—it was sooo delish. Thanks, Jenn, for yet another wonderful recipe 😋
The spaghetti squash were huge in the store so I bought the smallest and had a full half left over. I removed it from the skin and refrigerated it. What to do with it now? I found your recipe. I sprayed the bottom of a 9×7 glass pan. In a bowl, I mixed squash, marinara sauce, salt, pepper, oregano and garlic. Once in the pan, I added various shredded cheeses, store bought bacon bits and topped that with the prepared Panko crumbs. 425 for half hour. It was DELICIOUS. I have leftovers for tomorrow. You can save the squash’s baking time by cutting the squash in half and putting both on a microwave safe plate with flesh down and piercing a few holes for venting. Times vary depending on size. Thank you so much for this recipe.