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 just. so. cheesy.

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 sautéing 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!

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Mushroom thy Bolognese!

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If you make this recipe, please feel free to share a photo and tag @The.Roasted.Root on Instagram!

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

Mushroom Bolognese Spaghetti Squash Casserole

4.50 from 38 votes
A meatless spaghetti squash casserole recipe with mushroom bolognese sauce
Prep Time 40 minutes
Cook Time 1 hour 30 minutes
Total Time 2 hours 10 minutes
Servings: 4 servings



  • 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


  • Roast the spaghetti squash according to these instructions, or cook the spaghetti squash using your preferred method.
  • 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.
  • 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.
  • 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).
  • 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.
  • Preheat the oven to 400 degrees F and lightly spray or oil a small casserole dish (9-inch square or round will work great!).
  • 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.
  • Bake on the center rack of the preheated oven for 30 to 45 minutes, until cheese is golden brown and sauce is bubbling.
  • Remove from oven and allow casserole to sit 30 minutes before serving.



*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.


Serving: 1of 4 · Calories: 350kcal · Carbohydrates: 23g · Protein: 19g · Fat: 21g · Fiber: 6g · Sugar: 11g
Author: Julia
Course: Main Dishes
Cuisine: American
Keyword: dinner recipe, gluten free, grain free, low-carb, spaghetti squash, spaghetti squash casserole, vegetarian
Did You Make This Recipe?I want to see it! Tag @the.roasted.root on social media!
Mushroom Bolognese Spaghetti Squash Casserole - a healthy vegetarian dinner recipe - low-carb, nutritious, grain-free

Julia Mueller
Meet the Author

Julia Mueller

Julia Mueller is a recipe developer, cookbook author, and founder of The Roasted Root. She has authored three bestselling cookbooks, – Paleo Power Powers, Delicious Probiotic Drinks, and The Quintessential Kale Cookbook. Her recipes have been featured in several national publications such as BuzzFeed, Self, Tasty, Country Living,, etc.

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4.50 from 38 votes (36 ratings without comment)

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Questions and Reviews

  1. My 3 favorite cheeses! I cannot wait to try this. Love the idea of a mushroom bolognese for a meatless meal!

    1. Yaaas! The Ricotta-mozzarella-parm trifecta is near impossible to beat! The mushrooms make the sauce soooo tasty! Lemme know if you try it! 😀

  2. Well I’m always happy to talk about (eat) cheese – Love the the stuff! This looks simply beautiful!! If I were going to run any type of a marathon – this is what I’d eat!

  3. I mean, I just posted an alfredo sauce, sooo…YES CHEESE! ALL THE CHEESE. Love how comfortful this looks!

  4. That half marathon sounds like a major feat and I hope you find a running partner! There’s always room for cheese in my diet so I’m loving this gorgeous casserole Julia! Mushrooms and spaghetti squash are favorites of mine so this is looking very good!

  5. Dang! That looks so good! I feel like so many folks I know are in the same January funk. Super proud of you for signing up for the half marathon and hip hop class!! I need to jump start my fitness and those are great motivators! Cheering you on from here!

  6. That mushroom bolognese sounds so freaking good! I hear you- this is a rough time for any kind of cleanse with it being so cold. All I want to do is curl up with a big bowl of comfort food and cheese is my weakness. 😉

    Have fun training for that half marathon, lol! You’re such an inspiration, lady. 2K feet is no joke!

  7. Sticking to goals, yas, until a cold thwarted me…. but I’m not giving up so easily! I’m still in… and I will say yasss to cheese. This looks scrumptious, Julia and I think just what I need to get my otherwise squash adverse husband to eat squash! Delicious work!

  8. 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!

  9. 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!

  10. 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!

  11. 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

  12. 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!!

  13. I substituted Rao’s bolenese sauce but included sauted mushrooms onions garlic and italian herbs came out great! A keeper recipe

  14. This recipe is one of our favorite go to dinners! It is hearty and healthy. It also refrigerates well if you have leftovers and is just as good the second time around! Thanks.

  15. Yummy. I don’t understand how omitting only the Parmesan cheese makes this dish vegetarian. All of the cheeses listed come from animals. Meatless, yes.

    1. Hi Brenda,

      Most cheeses are vegetarian (since they’re made from milk and not animal meat). Parmesan cheese is not vegetarian as animal rennet is used in the processing of it. In this sense, the recipe is vegetarian without the parmesan cheese, and can easily be made vegan by swapping all the cheeses for vegan versions. Hope this makes sense! xo

  16. Can you freeze this dish? Or would you freeze this recipe up to a certain point and then add the cheese when it’s time to bake it?

    1. Hi Laurie! Either option will work 🙂 If it were me, I would probably make the whole recipe and then freeze it, but it’s up to you if you’d rather add the cheese after reheating it 🙂