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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My husband and I like this recipe! Would it work to make it up until the baking point, and then put in the refrigerator, and then bake later? What would you suggest to prep this for dinner ahead of time? (In the morning or day before)
Hi Heather, I definitely think you could assemble this ahead and refrigerate. If given the choice, I’d probably do it the morning before (and glad you like it)!
Absolutely delicious! You cannot overcook. Let it get nice and browned. YUMMMMM
Easy to make and absolutely delicious. Loved it.
Jenn, your spaghetti squash recipe was AWESOME! I followed the recipe exactly (even using Rao’s marina sauce which I could have eaten out of the jar) …no substitutes! It was a BIG hit with my family …my son-in-law went back for seconds, or was it thirds?
How will this hold up if I assemble it one day and bake & eat it the next? Or will it be better if I assemble & bake one day and reheat the next? Thank You.
Hi Kate, I think you could go either way with good results. Hope you enjoy!
I do not like to buy marinara sauces, too much salt and sugar. Any suggestion for best home made version that would have right texture for these recipes?
Hi Susan, This one would work well.
Spaghetti squash is difficult to find here in Portugal, could ordinary butternut squash be used instead in this recipe?
Unfortunately, because butternut squash doesn’t form spaghetti-like strands, it won’t work here– sorry!
Does this freeze well?
Hi Karen, I’ve never frozen this so I can’t say for sure, but I suspect you could freeze it.
My roommate and I just discovered the joy of squash and have enjoyed the leftovers of this recipe everyday for fantastic lunches!
This was my first experience with spaghetti squash. I’ve been skeptical, but how exciting that it really does work as a delicious pasta substitute! I made this with my homemade tomato sauce with sausage, au gratin per Jen’s recipe. The following week, I used the other half of the squash (which I had frozen) with a white clam-and-shrimp sauce. Also incredible! I think next time I’ll try without cutting the squash in half so that I can get nice, long “noodle” strands. Fabulous.
OMG!!!! Have tried to make spaghetti squash 2-3 times over the years and have been more than a little disappointed. No more! I just made this recipe, using ingredients I had on had (i.e., no panko bread crumbs, just plain; mozzarella and cheddar, no Italian cheese blend; and I had a meat sauce in the freezer).
Can I say I’m moaning with delight in every bite!!!! Cannot wait to take leftovers to work and share the love. This recipe is a hit.