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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Delicious!! Recipe is a keeper. Froze leftovers and they were tasty also.
This is terrific!! I had jalapeño jack cheese on hand and used that rather than mozzarella. Added a nice little kick. This will definitely be a go-to weekday dinner.
“World class” was my husband’s comment and I certainly agree! I had almost given up on spaghetti squash as it normally is very bland. Not this dish! You should have heard two carnivores roaring over this vegetarian delight.
Hi Jen, I love all your recipes and I credit you for making me a much better cook. I’m so glad you said to get two smaller size squash, It took all my strength to cut them. Because of you I’m getting a little more adventurous and last night I added leftover rotisserie chicken and sautéed some bell peppers and made this our main dish. My husband usually doesn’t like squash and he loved this dish. Thank you again.
This is fantastic. Mixing the marinara sauce with the spaghetti squash is brilliant- low fat. All of the “decadence” is on the top and shines. Thank you so much for all of your fantastic recipes and generosity. I know anything I make from your books or website is going to be delicious.
❤️
Unbelievably delicious as are all of Jenn’s recipes. My husband ate half of the 9 x 13 pan himself in one sitting. Points I would like to add and not sure if this was mentioned by another reviewer is to drain the strands once they are cooled and out of the shell. Had I not done that, it would have been too watery. In addition to the two 2.5 lbs of squash, I also added another small one to ensure there was plenty of squash to balance with all those (not so healthy) toppings. Super yummy.
I tried this and it was a hit. We served it with with Italian meatballs, but this would be a great side dish for fish or shrimp. There are only two of us but the leftovers were even better the next day. I will be making this the next time we have dinner guests as it can be made ahead. Bonus….The flavour is better the next day.
Really delicious dish. I had it for my main course and my husband and daughter ate it with Italian sausage and salad. I used vegan Parmesan to make it vegetarian. I wasn’t sure that they would like it, but both of them had seconds! If you roast the squash ahead of time, it all comes together in no time. Thanks for a great recipe!
Lonely spaghetti squash on my counter, and in comes this recipe. Oh my goodness! Absolutely delicious (and I am very much not a spaghetti squash fan!). I used Rao’s marinara. Don’t skimp on the thyme, it makes the dish. I already have plans to use this over Thanksgiving week with guests.
Hi Jen – I’ve been making your Spaghetti Squash Au Gratin recipe for years now & love it! I noticed you’ve replaced it with this recipe, which is similar yet slightly different (e.g., baking the squash as opposed to boiling). I’m sure it’s delicious (as all your recipes are). Out of curiosity, why did you make the change? Does it change the taste/nutritional value in some way?
Hi Lily, Sometimes the boiling method leaves the squash a bit watery, so these days I tend to roast it (I originally posted the recipe in 2009!). The flavor is a little more concentrated with the roasting method, as the sauce doesn’t get diluted, but it’s not a huge difference. Hope that helps! 🙂