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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I have made this twice already, and last night when I served it my husband exclaimed, “Yay! You made my favorite dish!” My husband cannot eat gluten, and this tastes much better than any rice pasta we have made. I love it also and did not feel guilty indulging in seconds. Instead of the panko, I used Aleia’s brand seasoned GF breadcrumbs – still tasted delicious without the gluten! I prepped the squash earlier in the day – you can boil it and scoop out the spaghetti strands and put them in the refrigerator until you are ready to combine them with the other ingredients and bake. Saves time and effort at dinnertime!
Hi Heather! Have you tried Jovial GF pasta? It’s my favorite! ~Julie
I second the Jovial recommendation. My current favorite is Ronzoni. I’ve even used it in recipes for non-gluten-free friends, and they can hardly tell the difference.
Jenn, you are a genius! This dish was amazing and even my kids ate it.
This recipe was incredible!!! I have never cooked spaghetti squash before and this method was full proof. I truly felt like I was eating spaghetti and knowing I could eat more and more without the guilt, was amazing!!! Thanks for this recipe, you made my day!!!
Made this for dinner last night and my whole family loved it. I never made spaghetti squash before but always wanted to try. Thanks!
This was yummy.
I used freshly grated fontina, asiago and some Parm for the cheese topping, and the panko bread crumbs gave it a nice crunch.
When I made this (years ago) I baked it, and it came out mushy. With your boiling method, the strands were perfectly separated and held their shape. Love it.
I served it with meatballs so my meat loving hubby would not be asking “Where’s the beef?” LOL (he loved it btw)
Love squash – love cheese/cream — can wait to try this one
http://mydinnerswithrichard.blogspot.com/
Looks amazing!
I recently made this using a lite alfredo sauce, mushrooms and grilled chicken. My husband thought I was a culinary god – he was totally mesmerized.
I’m glad to get your reminder about spaghetti squash. It’s a great dish that somehow got dropped from my already sparse repertoire. And the instruction for cutting it will prevent the awful mess I made the first time I made it.
Thanks.
I’ve been obsessed w spaghetti squash lately. That looks great, will have to try it asap. =)