Spaghetti Squash Casserole

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This easy Spaghetti Squash Casserole is the perfect, savory, cheesy, and delicious dish! Made with a handful of simple, nutritious ingredients, it requires minimal prep time and makes enough to feed the family. Serve it as a satisfying, low-carb, side dish, or bulk it up with protein for a complete meal!

A cheesy spaghetti squash casserole with a spoon in it.

Scrumptious Spaghetti Squash Casserole

With cool weather right around the corner and all the fall produce starting to come into season, we knew it was time to bust out our favorite veggie and create something delicious, nutritious, and comforting.

Loaded with veggies and tossed with a hearty marinara sauce, it’s a filling, flavor-loaded dish you can feel good about. Plus, this squash casserole is:

Gluten-free, grain-free, and vegetarian.
Made with minimal prep time.
Great to enjoy as a side or main course.
Perfect to prep in advance and enjoy throughout the week.

Overhead photo of gluten free spaghetti squash casserole with a spoon in it.

Ingredients You’ll Need

You won’t find any powdered cheese or undesirable additives in this casserole recipe! Instead, we use whole food ingredients to create a savory flavor that will have all your guests practically licking their plates. Here’s what you need:

Halved spaghetti squash, marinara sauce, spinach and other ingredients on a white marble countertop.

For the Squash

Spaghetti Squash – Pick a spaghetti squash that’s free from any dark spots or discoloration and doesn’t have any cracks in the skin.
Sea Salt and Black Pepper – Adjust to taste.
Olive Oil – We like the peppery flavor that olive oil adds, but feel free to substitute avocado oil, if preferred.
Veggies – Chopped onion, broccoli, and baby spinach and color, bulk, and nutrients to the dish.

For the Sauce

Cream Cheese – For the best taste and texture, use plain full-fat cream cheese. Or, swap it out for dairy-free cream cheese, if needed.
Marinara Sauce – If you’re feeling ambitious, feel free to make homemade marinara sauce or nomato sauce. However, to save time, we just opt for store-bought.
Parmesan Cheese – For the best taste and texture, buy fresh parmesan and grate it yourself. Feel free to use a dairy-free substitute like nutritional yeast, if desired.
Seasonings – Garlic powder, onion powder, Italian seasoning, salt, black pepper, and red pepper flakes combine to create a savory flavor with just a hint of heat.
Optional Toppings – We love to add an extra sprinkle of parmesan and fresh parsley for garnish! However, shredded Mozzarella, Cheddar cheese, or basil would also taste great!

Pro-Tip: Add in cooked shredded chicken, ground beef or turkey, or pre-cooked nitrate free italian sausage to transform this recipe into a complete meal!

Health Benefits of Spaghetti Squash

One of the most versatile veggies, spaghetti squash is a great low-carb option for pasta, casseroles, and more. Not only is it versatile and easy to prepare, but spaghetti squash is also full of health benefits, too. For example, this fall and winter squash is:

A good source of fiber.
High in vitamin C and vitamin B6.
Rich in manganese, pantothenic acid, and niacin.
Low in carbohydrates, saturated fat, and cholesterol.

How to Make Spaghetti Squash Casserole

If you’ve ever avoided spaghetti squash casseroles because you’re not sure what to do, this casserole is for you! Although it requires a few steps, it’s easy to make and is virtually failproof.

Prepare. Before you begin, preheat your oven, and line a baking pan with aluminum foil.
Cook the Squash. Use a sharp knife to slice the squash in half (removing and discarding the seeds), and sprinkle it with sea salt. Place both halves cut side down on the prepared baking sheet, and roast them in the preheated oven until fork tender. Let the squash cool. Then, use a fork to pull the strings from the center, and transfer the strands to a large bowl.

Two halves of baked spaghetti squash on a baking sheet.

Two spaghetti squash halves filled with spaghetti squash noodles on a baking sheet.

Pro-Tip: Speed up the preparation time by making air fryer spaghetti squash instead! This is also the most effective method for removing excess water from the squash noodles so your casserole doesn’t become soggy!

Sauté the Veggies. Reduce the oven temperature, and heat part of the olive oil in a large oven-safe skillet or cast iron pan over medium-high heat. Add the onion, broccoli, spinach, and a pinch of salt and pepper. Cook until the veggies are tender. Then, transfer the veggies to the bowl with the cooked spaghetti squash.
Create the Sauce. Add the cream cheese, marinara, parmesan, and spices to the skillet used to cook the veggies. Stir to combine, and let the mixture simmer over medium-low heat until the cheese is melted and the flavors blend together.

Whisk in a pan of creamy marinara sauce for spaghetti squash casserole.

Spaghetti squash noodles and cooked veggies on a creamy marinara sauce in a pan.

Combine and Bake. Add the spaghetti squash mixture and cooked meat, if using, to the pan of sauce, and gently fold to combine and coat the veggies. Sprinkle shredded cheese on top, and transfer the skillet to the oven. Bake until the top is golden brown and bubbly.

Note: If you don’t have an oven-safe skillet, transfer the squash mixture into an oven safe casserole dish greased with cooking oil spray or olive oil. Then, cover the casserole with cheese and bake as normal.

Shredded cheddar cheese on top of an uncooked spaghetti squash casserole.

Overhead photo of two woman's hands holding a gluten free spaghetti squash casserole.

Serving Suggestions

If you add protein to this dish, it’s a complete meal on its own! Of course, you can never go wrong with a side of easy gluten-free rolls, though.

Or, enjoy it as a side with main courses like roasted corn soup, gluten-free chickpea burgers, gluten-free panko chicken, or cod cakes!

Up close photo of a spoon digging into a cheesy spaghetti squash casserole.

Make Ahead and Storage Options

This casserole makes five servings and stores super well, meaning it’s great for meal prep! Just follow the steps below to keep it fresh.

To Make Ahead: Feel free to roast the spaghetti squash ahead of time. Once cooled, the strands can be transferred to an airtight container and stored in the fridge for up to 2-3 days.
To Store: Once combined, the casserole can be transferred to an airtight container and kept in the fridge for up to 5 days.
To Reheat: Warm individual portions in the microwave. Or, heat large portions in a skillet over medium heat until your desired temperature is reached.

More of Our Favorite

Gluten-Free Casserole Recipes

Common Questions

How do you keep squash casserole from getting watery?

The best way to prevent your casserole from becoming watery is to cook the squash in the air fryer before combining the rest of the ingredients.

Does spaghetti squash taste like pasta?

Spaghetti squash is fairly bland and slightly sweet in flavor, meaning it takes on the taste of whatever it is paired with, often tasting like pasta when paired with pasta sauce.

Can you eat the guts of a spaghetti squash?

Yes, in fact, the entire squash skin and all is edible! Although, most people find the skin a little tough and unpleasant to consume.

Is spaghetti squash healthier than regular pasta?

Of course, what’s healthy looks different for everyone. If you have specific concerns, we highly recommend consulting your doctor. However, in general, spaghetti squash is considered a healthy, low-carb, high-fiber alternative, offering lots of vitamins and nutrients not found in pasta.

Can I freeze spaghetti squash casserole?

We don’t love to freeze this recipe as it can become a bit soggy once thawed. However, if you really want to, leftovers can be frozen for up to 3 months.

When you’re ready to eat, allow your casserole to thaw in the fridge overnight. Then, transfer the leftovers to a baking dish, cover it with foil, and warm in the oven at 350 degrees Fahrenheit until your desired temperature is reached. Remove the foil, and continue to bake until the top is golden and bubbly.

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