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Mushroom Bolognese Spaghetti Squash Casserole

 Comforting three cheese spaghetti squash casserole with mushroom bolognese sauce – an ultra pleasing gluten-free vegetarian meal. 


Three Cheese Mushroom Bolognese Spaghetti Squash Casserole - a comforting vegetarian meal | #glutenfree #recipe #dinner

This twice-baked spaghetti squash adventure is probably one of my favorite ways of preparing spaghetti squash.

It’s like lasagna, but without noodles.. like a casserole, but on the healthful end of the spectrum.. Like spaghetti bolognese, sans the spaghetti and sans the actual bolognese.

What it is is, is a comforting cheesy Italian-inspired vegetarian meal with a “bolognese” sauce using mushrooms in place of meat. Basically it’s its own animal, and truly, I think you all will love it.

And you guys…it’s

Mushroom Bolognese Spaghetti Squash Casserole - a comforting vegetarian meal | #glutenfree #recipe #dinner

Inspired by the Turkey Bolognese Stuffed Spaghetti Squash I posted a few years ago, this vegetarian version and casserole mash-up is a fun little game changer, and a brilliant make-ahead dinner for your busy workweek.

The recipe itself feeds 3 to 4 comfortably – if you need to feed more people, or are a huge fan of leftovers like me, feel free to double the recipe.

I’m going to give it to you straight…this recipe does require a chunk of time investment. It’s not the quickest to prepare, but on the upside, most of the ingredients requires are probably already in your pantry.

Plus, this recipe can also be made in parts by roasting the squash and/or preparing the sauce ahead of time.


Three Cheese Mushroom Bolognese Spaghetti Squash Casserole - a comforting vegetarian meal | #glutenfree #recipe #dinner

How to Make Mushroom Bolognese Spaghetti Squash Casserole:

First things first, we’re going to roast our spaghetti squash. For those of you who are new to this endeavor, check out my post on How to Roast a Spaghetti Squash.

While the squash is roasting in the oven, prepare the mushroom bolognese sauce. You can also prepare the sauce up to 5 days in advance for an even more flavorful experience, or to break the recipe into parts.

Once the squash is roasted, we spaghetti it, then place our squash noodles in a casserole dish. Top it with mushroom bolognese sauce and three our three cheeses – parmesan, mozzarella, and ricotta.

The casserole goes in the oven, and the end result is an ultra gooey, tomato-sauced pile of healthy noodles.

Recipe Tips:

  • During the baking process, the spaghetti squash “noodles” will become more watery, causing the sauce to be thin at the bottom of the dish. To alleviate this, you can either let the spaghetti squash noodles drain in a colander before using them in the casserole, or allow the casserole to sit for 30 minutes before serving.
  • To cut down some of the work, you can use store-bought sauce. To do so, omit the sauce ingredients with one large jar of your favorite store-bought sauce. You can still make this a mushroom bolognese affair by sauteing the mushrooms in a skillet and adding the store-bought sauce to bring it all together. 

Like all casserole/pasta dishes, this meal becomes even tastier the day after you make it, so if you’re willing to wait it out, try preparing it a full day ahead of time!

You May Also Love:

Mushroom thy bolognese!

My cookbook, Paleo Power Bowls, is now available! CLICK HERE to check it out. Thank you for your support!

If you make this recipe, please feel free to share a photo and tag @TheRoastedRoot on Instagram!

Three Cheese Mushroom Bolognese Spaghetti Squash Casserole - a comforting vegetarian meal | #glutenfree #recipe #dinner

Mushroom Bolognese Spaghetti Squash Casserole

Course: Main Course
Cuisine: American
Keyword: gluten free, grain free, low-carb, vegetarian
Prep Time: 40 minutes
Cook Time: 1 hour 30 minutes
Total Time: 2 hours 10 minutes
Servings: 4 servings
Calories: 350 kcal

A meatless spaghetti squash casserole recipe with mushroom bolognese sauce




  • 2 tablespoons olive oil
  • 1/2 large onion, finely chopped
  • 8 ounces baby bella mushrooms (or crimini mushrooms), quartered
  • 5 cloves garlic, minced
  • 1 teaspoon rosemary (fresh or dried)
  • 2 teaspoons dried oregano
  • 2 teaspoons paprika
  • 1/2 teaspoon red pepper flakes, optional
  • 1 teaspoon sea salt
  • 1 28-ounce can crushed tomatoes, undrained
  • 2 tablespoons fresh basil, chopped


  • 1 large spaghetti squash, roasted
  • 1 1/2 cups mozzarella cheese, grated
  • 1/4 cup Parmesan cheese, grated see note*
  • 1/3 cup ricotta cheese


  1. Roast the spaghetti squash according to these instructions, or cook the spaghetti squash using your preferred method.

  2. Prepare the mushroom bolognese sauce. In a large saute pan or pot, heat the olive oil over medium and add the chopped onion. Saute, stirring frequently, until onion his very fragrant and has softened, about 8 minutes.

  3. Add the chopped mushrooms and garlic, and saute, stirring occasionally, until very fragrant, about 3 to 5 minutes. Add the garlic, rosemary, oregano, paprika, red pepper flakes, and sea salt and cook another 2 minutes.

  4. Add the crushed tomatoes and bring sauce to a gentle boil. Reduce the heat to a simmer, cover, and cook 30 minutes (or longer to maximize flavor if desired).

  5. Remove the cover and cook at a gentle boil for 10 minutes, until sauce is thick. Add the chopped basil, stir, and set sauce aside until ready to use.

  6. Preheat the oven to 400 degrees F and lightly spray or oil a small casserole dish (9-inch square or round will work great!).

  7. Transfer the cooked spaghetti squash to the prepared casserole dish and sprinkle with sea salt. Pour the mushroom bolognese sauce over the spaghetti squash noodles, then top with the grated mozzarella, parmesan, and ricotta cheeses.

  8. Bake on the center rack of the preheated oven for 30 to 45 minutes, until cheese is golden brown and sauce is bubbling.

  9. Remove from oven and allow casserole to sit 30 minutes before serving.

Recipe Notes

*Omit the parmesan to make this recipe vegetarian. You can replace it with any of your favorite vegetarian (or vegan) cheeses, such as gouda, grueyere, sheep's milk cheese, etc.

Nutrition Facts
Mushroom Bolognese Spaghetti Squash Casserole
Amount Per Serving (1 of 4)
Calories 350 Calories from Fat 189
% Daily Value*
Fat 21g32%
Carbohydrates 23g8%
Fiber 6g25%
Sugar 11g12%
Protein 19g38%
* Percent Daily Values are based on a 2000 calorie diet.

Mushroom Bolognese Spaghetti Squash Casserole - a healthy vegetarian dinner recipe - low-carb, nutritious, grain-free

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Sunday 31st of January 2021

I’m making this for my Sunday dinner! Looking forward to it! — I was just wondering if you know what the calories would be without the dairy? (Mozzarella, Parmesan and Ricotta Cheeses?) Thank you!!


Thursday 29th of October 2020

so yummy and since I don't eaat cheese I made my own Ricotta with cashews and used daiya dairy free cheese no parm and it was still as delicious


Thursday 29th of October 2020

Oooh, I've been meaning to make dairy-free ricotta! Love it! Thanks for the inspiration! xo


Saturday 16th of May 2020

Thank you for sharing this wonderful recipe! I made this yesterday & it was outstanding. It’s an absolute keeper. I think you could also just use the mushroom bolognese with the spaghetti squash, sprinkled with some cheese, & it would be fantastic too. I’ll try that next time.

Thank you again!


Sunday 17th of May 2020

Yaaay That's great to hear, Amy! Thank you for the sweet note! xoxo

Kathy Medlar

Friday 4th of October 2019

This dish is a winner!!! We did add a pich of sugar to cut the acid from the tomatoes. Can't wait to try other recipes. My husband and I are transitioning to vegetarian. This was a wonderful start....Thank you!


Monday 7th of October 2019

I'm so thrilled to hear it, Kathy! The sugar was a fabulous idea. Many thanks for your sweet message! xo


Thursday 25th of October 2018

I made the mushroom bolognese and it was delicious!. My son is a vegetarian but my husband & I are not. We all enjoyed the dish. It is nice to have a go-to website for vegetarian meal options!


Thursday 25th of October 2018

I'm so happy your family liked it! Thanks for the sweet note! :D xo

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