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This easy spaghetti squash casserole is packed full of nutritious ingredients for a delicious family meal! If you are looking for a comforting vegetarian, gluten free recipe with all the classic flavors of a pasta bake, give this casserole a try!

When I think of comfort food, a good pasta bake or casserole is at the top of the list. Unfortunately, they aren’t always the best choice for a healthy dinner. My lightened up version is made with spaghetti squash for a gluten free main dish that works for a lower calorie diet. 

This healthy main dish has all the comfort and flavor of an Italian casserole, without the pasta! This baked spaghetti squash casserole recipe is easy to make, tasty, and totally family friendly.

It’s super cheesy, yet packed with veggies for extra nutrients and fiber for the perfect way to get in a boost of health. Whether you’re a vegetarian or a meat eater you’ll be completely satisfied with this filling and flavorful recipe. It will quickly become one of your favorite things to cook for an easy weeknight dinner! It is one of those classic fall recipes that can be enjoyed anytime of year.

Whether you are short on time or an amateur in the kitchen, this gluten free squash casserole is so simple to make! After 15 minutes of prep all you have to do is pop it in the oven to bake with a cooking time of 30 minutes.

The best part? This spaghetti squash gratin is super versatile with so many different ways to enjoy it! Try it out with different sauces, veggie combos, or even vegan cheese for a plant-based option.

👩🏽‍🍳 Why You’ll Love This Recipe

• Easy To Make: Throw this spaghetti squash lasagna casserole together in 15 minutes, and then sit back and relax while it bakes! 
• Lower Calorie Option: Since you are substituting traditional pasta in this recipe for spaghetti squash, you drastically cut the amount of calories you might find in similar pasta dishes.
• Gluten-Free: This cheesy spaghetti squash casserole is naturally gluten-free making it a good option for a range of dietary needs and preferences! 
• Packed With Nutrients: You will get plenty of vegetables with this meal, which means lots of vitamins, minerals, fiber, and more. Each serving has 16 grams of protein and 209 mg of Vitamin C! This is a healthy lunch or dinner option for the whole family.

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🥘 Ingredients

This vegetarian spaghetti squash casserole bake requires simple ingredients that you can easily find at the grocery store. See the recipe card at the bottom of this post for detailed instructions and nutritional data. 

• Spaghetti Squash: The star of this recipe, spaghetti squash is the best alternative to pasta when you want something light and nutritious.
• Olive Oil: Just a drizzle of olive oil is needed in this recipe to help saute the vegetables.
• Vegetables: This healthy casserole recipe calls for diced yellow bell peppers, chopped onion, diced carrots, zucchini, and garlic. 
• Italian Seasoning & Oregano: Any classic Italian spices will do but my favorites are a pre-mixed Italian seasoning and dried oregano.
• Crushed Red Pepper: Add a subtle spice to the this healthy spaghetti squash main dish recipe with crushed red pepper flakes!
• Black Pepper & Salt: Salt and pepper make every dish better! Use whatever type of salt you’d like in this recipe.
• Pasta Sauce: Use whatever sauce you prefer for this spaghetti squash pizza casserole. My favorite brands are Muir Glen or Cucina Antica. Looking for a sauce with no added sugar is great!
• Shredded Cheese: I recommend using an Italian blend of shredded cheese or shredded parmesan for this spaghetti squash cheese casserole to keep that authentic Italian flavor.

✔️ Ingredient Substitutions

• Gluten Free Pasta Noodles: Although this is a recipe for spaghetti squash casserole, the veggies and other ingredients would pair perfectly with any type of pasta instead of spaghetti squash too! Use gluten free pasta to keep this recipe gluten free friendly.
• Calabrian Chile Peppers: Another fun idea to add spice instead of crushed red pepper flakes is calabrian peppers! 
• Garlic Powder: No garlic cloves on hand? No worries! Get that garlicky taste with some garlic powder instead.
• Parsley: You can use parsley or other Italian spices in this healthy spaghetti squash recipe if you do not have any oregano.
• Meat Sauce: If you aren’t vegetarian or vegan, feel free to substitute your sauce for a meat option.
• Mozzarella Cheese: If you don’t have an Italian blend of cheese or parmesan handy, mozzarella on its own would be great too!

🔪 How To Make Spaghetti Squash Casserole

The hardest part about this dish is simply resisting the urge to eat the whole thing, but by all means do so if you are compelled! Here is how to make this creamy spaghetti squash casserole:

Preheat & Cook Squash: Preheat oven to 350ºF. Poke spaghetti squash all over with a knife and cook in the microwave on a microwave-safe plate for 8 to 12 minutes until soft. If you don’t have a microwave, place the poked squash on a baking sheet and bake at 375ºF for 45 to 60 minutes.

Saute Veggies: While the squash is cooking, add oil, yellow pepper, red onion, carrots, zucchini, garlic, Italian seasoning, dried oregano, crushed red pepper, and salt & pepper to a large pan. Cook over medium heat for about 10-15 minutes or until fully cooked through.

Prepare The Squash: Cut the squash in half with a sharp knife. Scoop out the seeds of each of the squash halves, and with a fork, scrape the flesh from the peel. It should flake off easily into spaghetti-like strands. 

Mix Ingredients: Place the spaghetti strands in a casserole dish. Add the cooked veggies, pasta sauce, and half of the cheese. Mix well. 

Bake: Once the oven temperature has reached 350 degrees, sprinkle the other half of the cheese on top of the casserole and bake this spaghetti squash au gratin for 30 minutes or until the cheese is bubbly.

Let Cool: Allow to cool for five minutes, serve, and enjoy!

💭 Expert Tips

• How To Cut Spaghetti Squash Open With Ease: Your first time prepping squash might feel tricky but it is easier than you think. Here’s how to cut a spaghetti squash open:
  • Using a sharp knife, poke a few small slits in the squash skin; poke in a dotted line along where you plan to slice the squash in half.
  • Microwave squash 8-12 minutes. Allow to cool slightly.
  • Place squash on a cutting board with the most-flat surface down. Slice off the stem, then slice along your ‘dotted line’ to cut it in half.
  • Scrape out the seeds with a spoon. Use a fork to pull the flesh away from the peel.
• Cut Squash Across The Middle For Longer Strands: The best way to cut the squash is across the middle When you cut it lengthwise you halve the strands, as they are arranged in a circular formation.
• Save Time: Cook the spaghetti squash in the microwave to reduce prep time, but you can also cook it in the oven.
• Use The Shells: Save the squash shell to use in place of bowls! Place individual servings into the halves and enjoy as spaghetti squash boats. This is a great way to cut down on dishes, too.

📖 Variations

• Enchilada Squash Casserole: Take a Mexican twist with this dish and transform it into an enchilada casserole. Substitute marinara sauce for enchilada sauce and the parmesan cheese for cheddar cheese. Add in black beans and top with sour cream.
• Creamy Garlic Squash Casserole: Boost the garlic flavors by using a garlic white sauce in this dish. You can also add extra garlic cloves or mix in creamy baked garlic.
• Gluten Free Spaghetti Squash Casserole With Meat: Feel free to add in your favorite meat to your spaghetti squash noodles like ground beef, ground turkey, or chicken breasts.
• Different Sauces: Try this gluten free spaghetti squash recipe with various sauces like this vegan bolognese, alfredo sauce without heavy cream, vodka sauce, or pesto without pine nuts. For an extra creamy sauce, mix in some cream cheese or even cottage cheese.

🍽 Serving Suggestions

This casserole stands on its own, but I personally love pairing it with some crusty bread and salad as a side dish. Here are a few more of my favorite serving suggestions:

🙌 Dietary Adaptations

This healthy spaghetti squash casserole recipe is already gluten free, vegetarian, and low carb but can be modified for other dietary needs.

Vegan Squash Casserole: If you are vegan, feel free to omit the cheese altogether or opt for a vegan cheese alternative.

Low FODMAP: If you follow a low-FODMAP diet, skip the onions and garlic and use your favorite sensitive stomach marinara sauce.

Keto Spaghetti Squash Casserole: This recipe has 31 grams of carbs and 8 grams of fiber per serving, for 23 grams net carbs making it a great recipe for a low carb diet but not quite keto. To make this keto friendly, modify the recipe by using a keto-friendly sauce (like this keto marinara sauce) and swapping some veggies for spinach, mushrooms, or cauliflower.

🫙 Storage Directions

You can store this spaghetti squash dish in either the fridge or freezer for tasty leftovers or meal prep! Here’s how to store and keep this cheesy casserole:

To Store In The Fridge: After the leftover spaghetti squash casserole has cooled to room temperature you can cover tightly with plastic wrap or foil and enjoy it as leftovers the next day. It will keep for about 2-3 days.

To Freeze: You can freeze this healthy squash casserole recipe for 2-3 months. Remove it from the casserole dish and transfer to an airtight container. I wouldn’t recommend a freezer bag since it won’t help the casserole hold together as well.

To Reheat: The next time you are ready to eat this gf squash casserole, reheat your casserole dish in the microwave, toaster oven, or regular oven. You may want to use a bit of cooking spray on your baking dish to avoid sticking. You could also heat this up on the stove top on medium heat or medium-high heat if frozen. Stir frequently.

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