This cheesy baked spaghetti squash casserole is a veggie-packed meal or side
dish you’re going to fall in love with! Tender spaghetti squash and mixed veggies
are layered with homemade tomato sauce, mozzarella, and Parmesan, then
baked until hot and bubbly. It’s an easy way to turn spaghetti squash into a
satisfying vegetarian dinner.

Squash your dinner rut
Spaghetti squash is the OG vegetable noodle, and I'm here to tell you it'd like to be baked up with a veggie-packed tomato sauce, smothered in cheese, and stuffed into your face like the delicious vegetarian comfort food it is.
I’m not going to tell you that spaghetti squash tastes exactly like pasta. It doesn’t! And it doesn’t need to. Once those tender squash strands are tossed with a deeply flavorful tomato sauce (my Instant Pot Pasta Sauce is fab if you're short on time) packed with onions, garlic, carrots, and celery, then blanketed in mozzarella and Parmesan and baked until browned and bubbling, they become their own very delicious form of comfort food.
These vegetarian spaghetti squash casserole lands somewhere between baked spaghetti and a cozy vegetable casserole. Serve it as a vegetarian main dish with a green salad and some crusty bread, or as a hearty side dish. You can also cook the squash or assemble the entire casserole ahead of time, making it a perfect option for a weeknight dinner.

Let's make this spagetti squash casserole together!
Ok my friend, let me show you how easy this is. You'll find specific quantities of ingredients and detailed instructions in the recipe card at the end of this post. For now, join me for a scroll and we'll walk through it step-by-step.
Step 1: Cook your spaghetti squash
Brace yourself, folks. I cook my spaghetti squash in the microwave.
Trust me on this one, it's the easiest way to cook a super-hard squash like spaghetti squash. You just stab the squash a bunch of times with a sharp-tipped knife, put it on a microwave-safe plate, and zap it for 12-ish minutes.

Step 2: Make the pasta sauce
Start by sautéing your onions on a medium heat until they turn a nice golden brown colour. Add in the garlic, carrots, and celery, and cook until the vegetable are soft. Then add your white wine or vermouth. This will pick up all that great flavour from the bottom of your pan. Add the crushed tomatoes, and season with salt and pepper.

Combine the sauce with the spaghetti squash noodles, and transfer everything into a casserole dish.
Step 3: Bake your spagetti squash casserole
Bake for 30 minutes, until the sauce is bubbling up around the edges. Remove from the oven and add your cheese! Then return to the oven and bake for an additional 15 minutes, until the cheese is brown and bubbly on top.

Step 4: serve!
Let your spaghetti squash casserole cool for a few minutes when it comes out of the oven so you don't burn your mouth on that brown bubbly cheese (I know you know what I mean), and then serve alongside some pasta or nice crusty bread.

Vegetarian Spaghetti Squash Casserole
Ingredients
- 1 large spaghetti squash about 3lbs / 1400g
- 2 Tablespoons extra virgin olive oil
- 1 large yellow onion diced
- 2 cloves garlic crushed
- 1 large stalk celery finely diced
- 2 medium carrots finely diced
- ½ cup dry white wine or white vermouth
- 14 ounce can crushed tomatoes
- salt and pepper
- 8 ounce mozzarella shredded
- ½ cup finely grated Parmesan cheese
Instructions
COOK THE SPAGHETTI SQUASH
- Pierce your spaghetti squash several times with the tip of a sharp knife.1 large spaghetti squash
- Place the spaghetti squash on a microwave-proof plate, and microwave on high for 12 minutes, stopping to check on and rotate the squash every three minutes.
- Remove the squash from the microwave and let it cool until you're able to handle it comfortably.
- Slice the squash in half, and use a spoon to remove the seeds.
- Use a fork to shred the spaghetti squash flesh into "noodles" and transfer the noodles into a bowl.
MAKE THE SAUCE
- Preheat your oven to 350°F / 180°C at this point.
- Heat the olive oil over medium heat in a large heavy-bottomed skillet.2 Tablespoons extra virgin olive oil
- Add the onion, and cook, stirring often, until it is well-browned - about 10-15 minutes.1 large yellow onion
- Add the garlic, celery, and carrots, and cook for about 5 minutes more, until the vegetables are softened.2 cloves garlic, 1 large stalk celery, 2 medium carrots
- Add the white wine and stir the contents of the pan well to lift the flavour from the bottom. Allow the wine to evaporate almost entirely.½ cup dry white wine
- Add the crushed tomatoes, and stir to combine well. Season with salt and pepper.14 ounce can crushed tomatoes , salt and pepper
ASSEMBLE THE CASSEROLE
- Add the tomato sauce to the spaghetti squash noodles, and stir to combine well.
- Transfer to a 9x9 inch casserole dish.
- Place in the oven, and bake for 30 minutes. The sauce should be bubbling up around the sides at this point.
- Remove the casserole dish from the oven and scatter the cheeses over the top.8 ounce mozzarella, ½ cup finely grated Parmesan cheese
- Return to the oven and bake for an additional 15 minutes, until the cheese is browned and bubbly on top.
- Remove from the oven and let rest for 5 minutes before serving.
Notes
- Nutrition values are an estimate only.
- You're aiming for teeny tiny finely diced vegetables in this dish. Feel free to shred them or do the chopping in your food processor to save time.
- While this recipe calls for white wine, I seldom have white wine kicking around in the colder months, but I always have a bottle of white vermouth in the liquor cabinet and use them interchangeably for cooking.
- Can I make this recipe in advance? You sure can! You can prepare everything in advance and leave it in the refrigerator until you're ready to bake it.
- Tip! Cook the spaghetti squash ahead of time and this recipe will come together quickly.
- Can I freeze this recipe? To be honest, I don't love this recipe frozen and re-heated. I recommend you keep the leftovers in the fridge and eat them up within 3-4 days.



Claire says
OoOoOh this was so good! I made on Sunday night and have been eating for lunch with buttery semolina toast. I used veggie broth instead of wine and realized after I started making it that I didn't have nearly enough mozzarella. I chopped up muenster slices to put on top and I highly recommend! The sauce takes a bit of time, so if I need a shortcut I might just use a chunky marinara in the future. Yum!
Christine says
My goodness is this ever delicious! My tiny human who is 3 wanted to help, and then when it was done, gobbled it right up! This has definitely moved into my recipe rotation- but I agree, low carbs makes me ragey. We ate with bread 😉
Katie Trant says
Yes! It's definitely my favourite way to eat spaghetti squash and a side of delicious crusty bread is an absolute must.