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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

ingredients for baked spaghetti squash with marinara

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). stem end cut off spaghetti squash

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).

slicing upright squash

Using a soup spoon, scrape out the seeds and discard them.

removing the seeds

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.

seasoning squash with oil, salt, and pepper

Flip the squash halves so they are cut-side-down.

squash cut side down on baking sheet

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.

roasted spaghetti squash

Use a fork to scrape out and fluff the strands.

scraping and fluffing stands

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.

spaghetti squash in bowl with sauce and seasonings

Toss gently until the squash is evenly coated. Taste and add adjust seasoning if necessary.

spaghetti squash mixed with sauce and seasoningsStep 4: Assemble and Bake 

Transfer the mixture to a 9 x 13-inch baking dish.

spaghetti squash in baking dish

Sprinkle the mozzarella cheese evenly over top, followed by the Parmigiano-Reggiano.

sprinkling cheese over top of squash

In a small bowl, combine the melted butter with the panko, and mix until the panko is evenly coated.

panko and butter mixture

Sprinkle the panko mixture evenly over the cheese.

ready to bake with crispy panko toppingBake for 25 to 30 minutes, or until the top is golden.

baked spaghetti squash with marinara sauceLet 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.

Servings: 4 to 6 as a main course, 8 as a side dish
Prep Time: 15 Minutes
Cook Time: 1 Hour 5 Minutes
Total Time: 1 Hour 20 Minutes

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

  1. 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.
  2. 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).
  3. Using a soup spoon, scrape out the seeds and discard them.
  4. 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.
  5. Increase the oven temperature to 425°F.
  6. 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.
  7. 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.
  8. 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

Powered by Edamam

  • 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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Comments

  • Absolutely delicious! Neither my husband nor I really care for spaghetti squash, but my daughter made it for her family and raved about it. And we heartily agree!

    • — Michael E on October 20, 2022
    • Reply
  • This was the first time I used spaghetti squash and I decided to try your recipe. I followed it exactly and really enjoyed it!
    The kids first looked suspiciously, but in the end, came for seconds! 🙂
    I paired it – as you suggested – with the Italian salad, and the dressing is to die for! Even my salad-skeptical daughter took seconds of the salad!
    Both recipes are total winners! 🙂 Thank you!

    • — PJ on September 8, 2022
    • Reply
  • This recipe helped me get my husband to love spaghetti squash. I did modify it a bit by adding hot Italian sausage to the sauce but it came out delicious! Thank you, Jen.

    • — Lulu on August 27, 2022
    • Reply
  • Made this recipe tonight with some changes and it was delicious. I had a smallish squash so halved the ingredients. Used italian seasoning instead of thyme, added one crumbled Italian sausage and a scoop of ricotta. I realize these were quite a few modifications but the recipe was a really good base to work from. Will definitely make this again or some version of it.

    • — Adrienne on March 28, 2022
    • Reply
  • Another winner Jenn! This was terrific! My only add was to brown some turkey Italian sausage and add the crumbles to the marinara sauce. This was one very tasty dish! Thanks for sharing the recipe!

    • — Jim Orvis on February 22, 2022
    • Reply
  • Like all of Jen’s recipes, another instant family favorite! I did add some diced Turkey pepperoni, but would have been just as good without it. I think sliced mushrooms would also be good!

    • — Jean C Kennell on February 18, 2022
    • Reply
  • 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!!

    • — Judi on February 18, 2022
    • Reply
  • 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!

    • — Joan Feder on February 17, 2022
    • Reply
    • 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).

      • — Connie Owen on October 16, 2022
      • Reply
  • 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!

    • — Meredith on February 11, 2022
    • Reply
  • 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!

    • — Christie on January 31, 2022
    • Reply
  • This recipe sounds divine! I’m wondering how cooked shrimp would taste with this since I have some to use up.

    • — Terry on January 6, 2022
    • Reply
    • Sure, Terry, that should work. Please LMK how it turns out!

      • — Jenn on January 6, 2022
      • Reply
  • This recipe was so good and great for a healthy, quick weeknight meal!

    • — Aisha on January 3, 2022
    • Reply
  • 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!

    • — Ashley on December 6, 2021
    • Reply
  • 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!

    • — Sandy on December 2, 2021
    • Reply
  • I’m trying to implement meatless Mondays. This will be perfect—it was sooo delish. Thanks, Jenn, for yet another wonderful recipe 😋

    • — Katrina Pilz on November 21, 2021
    • Reply
  • 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.

    • — Roseria Wergin on November 17, 2021
    • Reply

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