Spaghetti squash casserole in a baking dish with a wooden serving spoon.

Spaghetti Squash Casserole

Author: Stephanie Kay

With over 25 grams of protein per serving, this baked spaghetti squash casserole recipe is a healthy, high-protein, low-carb, and low-calorie meal. Plus, it keeps well in the fridge and freezer, which makes it great for meal prep.

  • Author: Stephanie Kay
  • Prep Time: 15 mintues
  • Cook Time: 1 hour
  • Total Time: 0 hours
  • Yield: 6 slices 1x
  • Category: Dinner
  • Method: Baked
  • Cuisine: American
Units Scale



  1. Preheat the oven to 400°F, line a large baking sheet with parchment paper, and grab a 9×13-inch baking dish.
  2. Place the spaghetti squash horizontally on a cutting board, and slice each of them widthwise into 2-inch rings. Once the rings have been cut, use a spoon to remove any seeds.
  3. Transfer the squash rings to the baking sheet, season them with a bit of salt, and then transfer the baking sheet to the oven for 40 minutes or until the squash is tender.
  4. While the squash is baking, prepare the meat sauce. In a large pot on medium-high heat, warm the olive oil, then add the ground beef and cook for 4-5 minutes until browned.
  5. Add the onion to the beef and continue to cook for 2-3 minutes until tender, add the red bell pepper and cook for an additional 1-2 minutes, then add the garlic, basil, oregano, thyme, red pepper flakes, salt, and black pepper, and cook for a final minute until fragrant.
  6. Add the crushed tomatoes and tomato paste and stir to combine with the ground beef mixture, then reduce the heat to a simmer and continue to cook, uncovered, until the spaghetti squash is ready.
  7. Once the spaghetti squash is cooked, remove the baking sheet from the oven, and allow it to cool for a few minutes. When the squash is cool enough to handle, using a fork, pull the squash flesh away from the skin to create noodle-like strands.
  8. Remove the meat sauce from the heat, transfer the spaghetti squash strands to the pot, and gently stir to combine.
  9. Transfer the ground beef and squash mixture to a 9×13-inch baking dish, spreading it out evenly, then sprinkle the top with mozzarella cheese and parmesan cheese.
  10. Transfer the baking dish to the oven to bake for 20 minutes, until the cheese is melted and the top is golden brown.
  11. The spaghetti squash casserole can be served immediately, with a sprinkle of fresh basil on top, or cooled and stored in the fridge for up to 4 days or in the freezer for up to 3 months.


To Use Onion Powder: Omit the onion and add 1 teaspoon of onion powder along with garlic and herbs in step 5.

To Use Garlic Powder: Omit the garlic cloves and use 1 teaspoon of garlic powder.