Cheesy Spaghetti Squash Casserole

This Cheesy Spaghetti Squash Casserole is loaded with cheese, fresh sage, and roasted red peppers. This vegetarian casserole makes a rich, decadent main dish or the perfect vegetarian holiday side.

By
Sally Vargas
Sally Vargas
Sally Vargas

Sally is the author of four cookbooks and is a regular correspondent for the Boston Globe Wednesday Food Section. She also is a food photographer.

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Updated October 26, 2022
Sally Vargas
Sally Vargas

This Spaghetti Squash Casserole was a big hit at a potluck recently where there were more than a few vegetarians around the table, and it would be a welcome addition during the holidays.

What's not to love about a tender squash, creamy cheese, fresh sage, and red peppers?

What Is Spaghetti Squash?

Just to be clear, spaghetti squash is a vegetable! It looks a bit like a large, yellow melon, but when you cut it open, pale yellow spaghetti-like strands lurk under the seeds. You could say spaghetti squash is kind of cool.

But let’s be perfectly honest. It's also a bit on the bland side, in the way zucchini is bland, but with a totally different texture.

Unlike the bold, intense flavors of butternut or acorn squash, spaghetti squash is like a blank canvas, waiting to be infused with flavors. It’s a great alternative for 'squash haters'—they will immediately be converted when they taste this cheesy casserole.

How To Cut and Cook a Spaghetti Squash

Spaghetti squash is a member of the gourd family, which means the outer shell is very tough. I use a few tricks to make cutting the squash easier. When you are finished cutting it, you want two long halves.

  • On a cutting board, set the squash on a folded dishtowel to keep it stable.
  • Hold the squash steady with one hand, and insert a large chef’s knife into the center of the squash the long way, and push it down to cut the squash in half.
  • If you find you have trouble cutting the squash into even halves, try first scoring a line or making several deep slits with your knife around the squash (from end to end) and then use that as a guide for cutting.
  • Once you have two halves, scrape out the seeds with a sharp-edged spoon and discard (or roast) the seeds. Place the halves with the cut sides down on a parchment lined baking sheet and bake.
Overhead view of cheese spaghetti squash casserole
Sally Vargas

Make Ahead Tips for This Casserole

OPTION 1: Prep the different components ahead of time.

  • You can prepare the components of the casserole (bake the squash, make the egg and cream mixture, cook the peppers and onions, grate the cheese) up to three days ahead of time and store each component separately in the refrigerator. Assemble and bake as directed in the recipe.

OPTION 2: Refrigerate the baked casserole.

  • Assemble and bake the casserole. When cooled to room temperature, cover with plastic wrap and refrigerate for up to three days. Reheat in a 350oF oven for 20 minutes, or until the casserole is hot all the way through.

OPTION 3: Freeze the baked casserole.

  • Assemble and bake the casserole. When cooled to room temperature, cover with plastic wrap and then foil, and freeze for up to two months. Defrost in the refrigerator overnight and bake at 350oF for 20 minutes, or until the casserole is hot all the way through.
Sally Vargas

Need More Vegetarian Recipes?

Cheesy Spaghetti Squash Casserole

Prep Time 60 mins
Cook Time 45 mins
Total Time 105 mins
Servings 6 to 8 servings

Ingredients

  • 1 tablespoon olive oil plus more for the baking dish

  • 1 spaghetti squash, about 3 pounds

  • 2 teaspoons kosher salt

  • 1/2 teaspoon freshly ground black pepper

  • 1 onion, finely chopped

  • 1 clove garlic, minced

  • 1/2 cup jarred roasted red peppers, thinly sliced

  • 2 tablespoons chopped fresh sage leaves

  • 3 large eggs

  • 1 cup whole milk

  • 3 tablespoons all-purpose flour

  • 1 1/2 cups (5 ounces) grated Jarlsberg or baby Swiss cheese

  • 1/2 cup (2 ounces) finely grated Parmesan

Method

  1. Preheat the oven:

    Preheat the oven to 425°F. Line a baking sheet with parchment. Brush or spray a shallow 2-quart baking dish with oil.

  2. Roast the squash:

    Cut the squash in half lengthwise and scrape out the seeds. Sprinkle with 1/4 teaspoon salt and 1/8 teaspoon pepper. Place on the baking sheet with the cut sides down. Bake for 30 to 40 minutes, or until the squash is tender when pierced with the tip of a paring knife.

    Remove from the oven and turn the squash so the cut sides are facing up. Return the squash to the oven and bake for another 5 minutes to dry out any excess liquid. (The squash won’t necessarily look dry.) Remove and let cool.

    Sally Vargas
  3. Cook the other ingredients:

    In a large skillet set over medium heat, add 1 tablespoon of oil. Once the oil begins to shimmer, add the onions, 1/4 teaspoon salt, and 1/4 teaspoon pepper. Cook, stirring occasionally, for 5 minutes or until softened.

    Stir in the garlic, red pepper slices, and sage. Cook and stir for another minute. Transfer to a large bowl.

    Sally Vargas
  4. Make the egg mixture:

    In a blender (immersion or countertop), pulse the eggs, milk, flour, 1/2 teaspoon salt and 1/8 teaspoon pepper 3 to 4 times, or until the mixture is smooth.

  5. Mix it all together:

    With a fork, flake the squash strands into the bowl on top of the onions. Add 1 teaspoon salt and mix until combined. Add the egg mixture, grated Jarlsberg cheese, and 1/4 cup of the Parmesan to the squash. Stir to combine.

    Sally Vargas
    Sally Vargas
  6. Bake the casserole:

    Transfer the squash mixture to the baking dish and sprinkle with the remaining 1/4 cup Parmesan. Bake for 40 to 45 minutes.

    Sally Vargas
  7. Serve:

    Let rest for 10 to 15 minutes before serving as a side dish or a vegetarian main.

Nutrition Facts (per serving)
231 Calories
13g Fat
16g Carbs
13g Protein
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Nutrition Facts
Servings: 6 to 8
Amount per serving
Calories 231
% Daily Value*
Total Fat 13g 17%
Saturated Fat 6g 31%
Cholesterol 98mg 33%
Sodium 630mg 27%
Total Carbohydrate 16g 6%
Dietary Fiber 2g 8%
Total Sugars 6g
Protein 13g
Vitamin C 22mg 111%
Calcium 321mg 25%
Iron 1mg 6%
Potassium 321mg 7%
*The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.
Nutrition information is calculated using an ingredient database and should be considered an estimate. In cases where multiple ingredient alternatives are given, the first listed is calculated for nutrition. Garnishes and optional ingredients are not included.