This baked spaghetti squash casserole is healthy and delicious. It’s easy to make vegan, vegetarian, or keto and is naturally gluten-free.

A ceramic Italian pasta dish filled with baked spaghetti squash noodles with tomato sauce.

Comforting baked pasta? That’s actually a vegetable? That pretty much sums up this spaghetti squash bake recipe. Let’s face it – kids love noodles, but a lot of us are trying to cut down on simple carbs like traditional spaghetti. 

This recipe is quite customizable. Go ahead and toss in any veggies or herbs you would like to use up. This week I added some fresh thyme and rosemary, and some cherry tomatoes on top since that’s what I had. Some cooked sausage (I used vegan Field Roast Italian sausage) is delicious thrown in with the veggies too. In the summer I add more bell peppers and some summer squash. 

A blue ceramic casserole dish filled with a vegetarian spaghetti squash bake with tomatoes and topped with parmesan cheese.

How to Make a Spaghetti Squash Casserole Bake 

This recipe does take longer than my usual dinners, as the squash takes about 45 minutes to cook. I recommend cooking the squash the night before, or in the morning to make things quicker at dinnertime. 

Once you have your cooked spaghetti squash “noodles” you’re ready to make the casserole. I love that this dish is so customizable. 

Spaghetti squash noodles with tomato sauce and cheese. A vegetarian spaghetti squash casserole.

More Spaghetti Squash

Yield: Serves 6

Vegetarian Baked Spaghetti Squash Casserole

Prep Time 5 minutes
Cook Time 1 hour 5 minutes
Total Time 5 minutes

Baked spaghetti squash casserole made with tomato sauce, cheese, and veggies is a tasty and satisfying vegetarian low-carb meal.

A blue ceramic casserole dish filled with a spaghetti squash bake.


  • 1 medium-sized spaghetti squash 
  • 2 tablespoons extra virgin olive oil, divided 
  • 1 small yellow onion
  • 3 cloves garlic, minced 
  • 1 red bell pepper, diced
  • 1 cup sliced crimini mushrooms 
  • 1 teaspoon oregano
  • 1 pinch red pepper flakes
  • 1 (26 ounce) box chopped tomatoes, such as Pomi
  • 1 tablespoon tomato paste
  • 1/4 cup fresh basil, chopped 
  • 8 ounces fresh mozzarella cheese packed in water, drained and cubed 
  • 1/4 cup grated Parmesan cheese 


  1. Preheat the oven to 400 degrees F. 
  2. Carefully cut the spaghetti squash in half lengthwise (this can be the hardest part). Brush or drizzle with 1 tablespoon olive oil. Season lightly with salt and pepper. Place cut side down on a baking sheet and roast for 45 minutes, or until tender. 
  3. Meanwhile, saute the onion in a large saucepan over medium-high heat with another tablespoon of olive oil until translucent. Add the garlic, bell pepper, mushrooms, oregano, and red pepper, and continue to saute until the vegetables have softened. Add the tomatoes and tomato paste, and simmer until slightly thickened, about 5 minutes. Stir in basil. Season sauce to taste with salt and pepper. 
  4. Use a fork to scratch "spaghetti noodles" out of the squash skin. Transfer "noodles" to a large casserole dish. Pour sauce over the top and stir in the mozzarella. Sprinkle Parmesan over the top and bake at 400 degrees for 20 minutes, until bubbly.  



  • To make this more like lasagna, add dollops of ricotta. I like Kite Hill vegan ricotta or homemade vegan ricotta best. 
  • For a meaty bake, add sliced or crumbled Italian cooked sausage.
  • Add sauteed sliced mushrooms, zucchini, eggplant, or any other favorite veggies. 
  • Add kalamata olives, capers, and red pepper flakes for a take on puttanesca. 
  • For a vegan bake, be sure to use only vegan cheeses.

Nutrition Information:
Yield: 6 Serving Size: 1 bowl
Amount Per Serving: Calories: 236Total Fat: 15gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 7gCholesterol: 33mgSodium: 347mgCarbohydrates: 17gFiber: 3gSugar: 7gProtein: 12g

Nutrition information is automatically calculated by Nutritionix. I am not a nutritionist and cannot guarantee accuracy. If your health depends on nutrition information, please calculate again with your favorite calculator.