Are you in need of a cheesy, pizza-like dish packed with veggies that isn’t pasta based, and that isn’t pizza? (I know, pizza that’s not pizza? Feels blasphemous to pizza!) You’ve come to the right recipe. And that recipe happens to be a stuffed spaghetti squash with cheese. It will feel like pizza in its flavors, but it doesn’t have any gluten or bread-like qualities.

This dish has it all! It’s easy to change up based on dietary needs and preferences (like all of our recipes). It’s also versatile in its use: stuffed spaghetti squash works well as a meal prep, and as something you can serve to guests.
How to customize stuffed spaghetti squash
First and foremost: You don’t have to use spaghetti squash. If you can’t find it or dislike it, PLEASE feel free to stuff an acorn squash, delicata squash, or butternut squash. Heck you could even use bell peppers or zucchini… the list goes on and on.
The spaghetti squash is just a good pick because it’s in season during the fall and winter and is generally something you can find in the grocery store most of the year. But that doesn’t mean you need to use it. I like it because it kind of mimics pasta without the pasta itself, so you can easily incorporate pasta-adjacent flavors and textures. And that’s kind of why I keep invoking pizza here!
You can easily make this vegetarian.
If you don’t eat meat, or you have vegetarian or vegan eaters at a meal you’re hosting/going to, you can replace the chicken with white beans or chickpeas! It’s one less cooking step for you, and the results equally as tasty.
Another option? Customize it even further, much like you would toppings on pizza! You can always do one half with meat and the other with legumes to please everyone at a holiday meal.
You can easily make this vegan.
By replacing the chicken with either more veggies or legumes and either using vegan mozzarella or skipping cheese altogether, you can make this meat and dairy free. You’d also have to use vegan pesto, which is so easy to make or find in stores like Trader Joe’s.
The cheese isn’t the star of the dish, so I honestly think this would be good without it!
Not into pesto?
Use a marinara sauce instead. No problem. Even a meat-based red sauce would work.
Not feeling tomatoes and kale?
Other veggies would work. Mushrooms, peas, chopped asparagus, Swiss chard, broccoli florets, etc. Spaghetti squash is very mild and pesto goes with pretty much everything!
I can’t think of a veggie that wouldn’t taste great with a little bit of pesto love!

How to serve cheesy spaghetti squash
The first thing I want to note is that if you serve this meal to guests, you’ll want to serve this to people soon after it comes out of the oven. This is the opposite of many stuffed dishes like lasagna or stuffed shells, for example.
So, if you’re planning to eat at, say, 6pm, pop it in the oven a little before 5 o’clock. If this stuffed squash sits for a bit before serving and eating, the cheese may harden a bit on top. And that’s not really very appetizing!
When serving, you can do a couple of different things. I sometimes like to cut the entire stuffed squash into portions for guests. If you’d prefer a more laid-back approach, have everyone scoop some of it out onto their plates, family style.
I like serving this with a nice green salad and/or some crusty bread.
How to make this spaghetti squash for meal prep
I used a quarter of a squash per serving (and got 4 servings total). I recommend waiting until the squash has cooled slightly to cut through it before dividing it among meal prep containers.
When you’re ready to eat this meal, you can do it a few ways. It reheats best in the microwave. You can reheat it as is and eat right out of the squash OR you can scoop what you’re going to eat out of the peel (because we don’t eat that part) and just reheat that. The latter is a little easier to eat, but either way works!
I also recommend adding a sprinkle of cheese before reheating. Because… you can never have too much cheese. And because it really benefits from some re-cheesing. (No that’s not really a word, but we’re going to pretend it is!)
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Cheesy Spaghetti Squash Stuffed With Tomatoes, Greens & Pesto
Ingredients
- 2 spaghetti squash cut it half, seeds scooped out
- 1 chicken breast
- 1 cup cherry tomatoes halved
- 2 cups spinach chopped, or kale
- 1 clove garlic minced
- 3/4 cup pesto or marinara, homemade or store bought
- Salt and pepper to taste
- 1 tsp dried thyme
- 1 tsp dried oregano
- 2 TBSP olive oil
- 15 oz can cannellini beans rinsed and drained
- 1 1/2 cups mozzarella cheese divided
Instructions
- Preheat oven to 400 F (200 C)
- Cut the spaghetti squash in half lengthwise. If you can heat it in the microwave for 2-3 minutes beforehand, it will be a lot easier. Scoop out the seeds with a fork and discard them. Drizzle olive oil over the each cut sides and add salt and pepper. Place the spaghetti squash pieces cut side down (aka face down) on a baking sheet and bake for 30 minutes.
- If using chicken: Place the chicken breast in a baking dish. Drizzle with olive oil, add salt, pepper and thyme. Turn the chicken over and repeat the process. Bake for 20-25 minutes, until the center is no longer pink or a meat thermometer reads 160 F.
- Add 1 tablespoon of oil to a skillet over medium heat. Add the garlic and let it cook, stirring often, for a few minutes. Then add the cherry tomatoes, greens, salt and pepper. Cook for about 5 minutes, until the greens have wilted. Transfer the cooked veggies to a bowl. If using white beans, add them to the bowl, too.
- When the chicken is done: let it rest for 10 minutes. Then chop the chicken into small pieces or shred with 2 forks. Add it to the bowl with the cooked veggies.
- Add the marinara or pesto and half of the mozzarella cheese to the bowl with the cooked veggies. Toss well until everything is combined.
- Scoop out and discard some of the spaghetti squash flesh to make room for the stuffing. Add a sprinkle of salt and pepper to the spaghetti squash, then divide the stuffing between the halves. It's okay if there's some overflow. Top with the remaining mozzarella cheese.
- Bake uncovered for 20 minutes, until the cheese starts to get a little brown. Serve immediately, or store let cool before slicing into portions for your meal prep containers!
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