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Vegetarian Spaghetti Squash Casserole Boats

Cheesy Spaghetti Squash Casserole Boats are stuffed with a creamy vegetarian spaghetti squash casserole. This vegetarian spaghetti squash recipe is the perfect cozy fall dish. 

Vegetarian spaghetti squash casserole boats with fork on wooden table

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Cheesy spaghetti squash is like the best thing ever. Would you agree?

What does spaghetti squash taste like? Well, if you’ve never had it, it really is similar to spaghetti, as the name implies!

It’s a cozy mixture of pasta-like strands, with CHEESE, obviously, and vegetables galore. I’m here for it and if you love vegetarian spaghetti squash recipes, you’ll love this. 

It’s a delicious easy winter squash recipe that we love!

We really enjoy new spaghetti recipes in our house, especially healthy stuffed spaghetti squash recipes.

This cheesy baked spaghetti squash gives my butternut squash beetroot salad a run for its money. But that’s a lighter option, whereas this cheesy garlic parmesan spaghetti squash is comforting and heavier. 

My biggest tip for these spaghetti squash boats is to buy your spaghetti squash from Trader Joe’s or somewhere where they don’t measure by weight.

You’ll save lots of money! Because they can get heavy, somewhere where you play a flat price is best. 

How to Roast Spaghetti Squash Whole

I used to be deathly afraid of cutting a spaghetti squash. It’s terrifying, to think of a big sharp knife missing its point.

I’ve learned a little bit since my early days. Now, to cut a spaghetti squash, I microwave it for a few minutes beforehand.

That’s the secret! It makes it much softer and more pliable to work with. In other words, you can cut into it much more easily.

Then, I like to lay it over a solid cutting board with a cloth over it to help keep it steady. And use a good quality knife

Sidenote: You CAN cook spaghetti squash in the microwave, though I think the oven version offers much more flavor and crispness.

But, we all know time is of the essence when we’re busy! If you need more easy dinner ideas for when you’re busy, check out this roundup for easy dinners

But, if you’re in a pinch and don’t have time to make this roasted spaghetti squash recipe, use the microwave!

Once you cut the squash in half, scoop out the seeds and place it open side up into the oven.

Then, you’ll get to making your filling for these taste vegetarian spaghetti squash boats. 

What You Need For A Vegetarian Spaghetti Squash Casserole Filling

The goal here is for the best cheesy garlic parmesan spaghetti squash filling. 

  • olive oil and/or butter (I used both)
  • white button mushrooms
  • one artichoke
  • cauliflower
  • edamame
  • garlic
  • yogurt
  • cream cheese
  • shredded cheese
  • breadcrumbs
  • spices of choice! I used s+p, paprika, Italian seasoning, garlic powder, chili powder

It’s the creamy, tasty, delicious combination of yogurt, cream cheese, and shredded cheese that makes these cheesy, vegetarian spaghetti squash casserole boats undeniably good.  

fork of cheesy spaghetti squash over spaghetti squash boat

How To Make the Filling For Vegetarian Spaghetti Squash Casserole

If you’re wondering how to cook winter squash, I’m partial to say this is one of my favorites.

The filling is really what we’re all here for, right? It really is the best version of a vegetarian spaghetti squash recipe. 

So, while the squash is cooking, start your veggie stuffing.

Add your mushrooms, cauliflower, and edamame (frozen veggies are fine) to a large skillet (I use this one). 

roasted vegetables in skillet for vegetarian spaghetti squash casserole

Then, add the garlic, yogurt, cheese, cream cheese, and seasonings. Give it a little shake and sautee everything so it mixes together and the flavors marinate. 

Once the spaghetti squash is done in the oven, scoop out the squash strands and seeds so you can add this stuffing!

Then, you’ll add the breadcrumbs and put them back in the oven for a crispy spaghetti squash finish.

cheesy stuffed spaghetti squash with breadcrumbs on wooden backboard

Can You Make Chicken Stuffed Spaghetti Squash?

Yes, there are several modifications you can make! Chicken will fit in nicely with the vegetables and cheesiness of the recipe. 

Other Modifications:

  • You can also leave out some of the vegetables or add in some other favorites to this cheesy baked spaghetti squash. 
  • Don’t like edamame? Try white beans, black beans, or garbanzo beans.
  • Need a dairy-free spaghetti squash recipe? Top with nutritional yeast instead of cheese. Swap the cream cheese and yogurt out for plant-based yogurt or cashew cheese. 
cheesy stuffed spaghetti squash with breadcrumbs on wooden backboard next to wooden spoon

The meal comes together in a little under an hour, so it is totally doable for a weeknight.

Plus, I’d suggest making a few at once to have leftovers throughout the week. It takes the same amount of time to cook two stuffed spaghetti squashes as it does four!

Lastly, I may suggest adding a little more cream cheese and yogurt for creaminess if you are heating up leftovers.

Nutrition of Spaghetti Squash 

Spaghetti squash is very nutritious and full of nutrients like Vitamin C, Vitamin A, and fiber. People use it as a pasta substitute because it has a similar texture when its strands are shredded, and since it is low carb, some people use it as a keto pasta recipe. 

The ingredients in these spaghetti squash boats are packed with nutrients as well. For example, did you know artichokes are a great source of prebiotics? They are! Prebiotics feed probiotics. 

artichoke on white background

Lucky for us, garlic and artichokes are full of prebiotics and other health-promoting compounds, too!

To stick with the gut theme, I also added yogurt in place of heavy cream for some additional probiotics and creaminess.

For more information on foods to improve your gut health, here’s what to look for in a probiotic. 

And if you want more probiotic-rich and delicious recipes, you may also like my vegan buddha bowl or banana chia pudding

Can You Freeze Spaghetti Squash Noodles?

Yes, absolutely, which is why this vegetarian stuffed spaghetti squash is great for meal prep and postpartum freezer meals!

Just let it cool at room temperature, and then place in freezer-friendly ziplock bags- we use these reusable freezer bags! When you’re ready to reheat, just toss them in a microwave safe dish or on the store. So easy!

I wouldn’t store it longer than 6 months. Here’s a more detailed post about freezing spaghetti squash

Other Squash and Fall Recipes

Yield: 4 servings

Vegetarian Spaghetti Squash Casserole Boats

cheesy stuffed spaghetti squash with breadcrumbs on wooden backboard

Vegetarian Spaghetti Squash Casserole Boats are stuffed with a creamy vegetarian spaghetti squash casserole. This vegetarian spaghetti squash recipe is the perfect cozy fall dish. 

Prep Time 10 minutes
Cook Time 50 minutes
Total Time 1 hour


  • 1 spaghetti squash, halved
  • 1-2 Tbsp olive oil
  • 2 Tbsp butter
  • 8-10 ounces white button mushrooms
  • One artichoke, diced (or use one 6-8 oz can)
  • 1 cup cauliflower, diced
  • 1 cup edamame (soybeans)
  • 2 cloves garlic, minced
  • 1/3 cup plain yogurt (I used full fat)
  • 3 Tbsp plain cream cheese
  • ¼ cup cheese (I used shredded parmesan)
  • ½ tsp sea salt
  • ½ tsp paprika
  • 1 Tbsp italian seasoning
  • ½ tsp garlic powder
  • 1/2 tsp chili powder, optional
  • salt and pepper, to taste
  • Parsley, optional
  • 1/3 cup breadcrumbs


  1. Preheat oven to 400
  2. Cut spaghetti squash in half, carefully. I like to microwave it for a few minutes to soften it up before cutting.
  3. Using a large spoon, scoop out seeds. Save these to roast later!
  4. Coat open ends with olive oil, salt and pepper and place face down in the oven for 35-45 minutes.
  5. While the squash is cooking, prepare your filling. Add butter to skillet over medium high heat. Add mushrooms, artichokes, cauliflower and edamame to skillet.
  6. Next, add garlic, yogurt, cheese, cream cheese, shredded cheese and seasonings. Saute until mushrooms are tender and sauce starts to bubble.
  7. Once spaghetti squash is done, scoop squash out and add to stuffing mixture. Add stuffing mixture back into squash boats and cover with breadcrumbs. Throw back in the oven for 5-10 minutes or until breadcrumbs are golden brown.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 461Total Fat: 24gSaturated Fat: 9gTrans Fat: 0gUnsaturated Fat: 12gCholesterol: 34mgSodium: 617mgCarbohydrates: 49gFiber: 18gSugar: 17gProtein: 23g

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spaghetti squash boats stuffed with veggies on wooden board

What’s your favorite type of squash? I think mine is a tie between spaghetti and butternut!

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