Cheesy Baked Spaghetti Squash
- By Jennifer Segal
- Updated October 5, 2026
- 99 Comments
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Cheesy, saucy, and topped with buttery crisp bread crumbs, this easy spaghetti squash bake is cozy, satisfying, and full of flavor.

Spaghetti squash earns its name once you roast it: the flesh pulls apart into tender, spaghetti-like strands that are naturally low in carbs and calories. Here, I toss the strands with good-quality jarred marinara sauce, top them with shredded cheese and crispy bread crumbs, and bake everything until gooey and golden brown. It makes a comforting vegetarian main course or a delicious 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 tackle. For this recipe, I use two medium squash rather than one large one, since the smaller squash are easier to cut.
“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!”
What You’ll Need To Make Cheesy Baked Spaghetti Squash

You’ll need two spaghetti squash, olive oil, jarred marinara sauce (I like Rao’s), shredded whole milk mozzarella, panko bread crumbs, Parmigiano Reggiano, butter, fresh thyme, salt, and fresh ground pepper.
How To Make Cheesy Baked Spaghetti Squash
Prep the spaghetti squash: Using a very sharp chef’s knife, cut a thin sliver off the stem end of the squash to create a flat surface. Stand the squash upright, then carefully slice down through the center from top to bottom, using your body weight to help press the knife through. Use a soup spoon to scoop out the seeds and stringy bits, then discard them.


Roast the spaghetti squash: Arrange the squash cut-side up on a baking sheet and season it, then flip it over so the cut sides are against the pan. Roasting it this way helps the squash brown and caramelize underneath. It’s ready when the flesh is tender and pulls easily into strands. Once the squash is cool enough to handle, use a fork to scrape and fluff the flesh into spaghetti-like strands.




Mix the squash with the sauce: Place the spaghetti squash strands in a large bowl, add the marinara and seasonings, and mix until the strands are evenly coated.


Assemble and bake: Spread the squash mixture in the baking dish, then top with the mozzarella and Parmigiano-Reggiano. In a small bowl, stir together the melted butter and panko until the crumbs are evenly coated, then sprinkle over the cheese. Bake until the cheese is bubbly and the panko is crisp and golden brown. Let cool for a few minutes, then sprinkle with fresh thyme and serve.




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Cheesy Baked Spaghetti Squash
Ingredients
- 2 medium spaghetti squash (about 2½ lbs/1.1 kg 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
Instructions
- Preheat the oven to 400°F (205°C) 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 (220°C).
- 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-in (23 x 33-cm) 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.
Notes
Pair with
Nutrition Information
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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It is crazy how good this dish is! Greater than the sum of its parts for sure. I used the Costco brand marinara and used fresh mozzarella rounds on top. I even forgot to add the last step with the breadcrumbs. The fresh thyme really pops!
Would your homemade tomato sauce recipe work in replacement to store bought sauce?
Thanks
Sure, Elizabeth, I think that should work. Hope you enjoy!