Cheesy Baked Spaghetti Squash with Marinara Sauce

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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 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 to meatballs or Italian sausage. To save time, I use a good quality store-bought marinara sauce, such as Rao’s or Victoria’s, as well as pre-shredded cheese.

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, since 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, using your body weight to press the knife down, to cut each squash in half.

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 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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