This cheesy Spaghetti Squash Casserole is cozy, hearty, and packed with hidden veggies. It features roasted spaghetti squash, spicy Italian sausage, lots of aromatics, and a rich tomato basil sauce. It’s folded together with creamy Greek yogurt and parmesan, then topped with melty mozzarella cheese. Every bite is savory, cheesy, and comforting—but still light and nutritious.
If you enjoy pasta and squash, you’ll also love my Butternut Squash Ravioli Sauce! This recipe takes only 15 minutes to prepare and is filled with brown butter, sage, champagne, and pecans. Pair it with your favorite store-bought ravioli for a quick weeknight dinner!
Enjoy quick recipes? Try my Spaghetti Squash in Air Fryer recipe. It is a great, healthy, and low-carb dinner recipe. It takes less than 30 minutes to roast the squash in the air fryer and comes out perfectly caramelized and tender.
Table of Contents
Why You’ll Love This Recipe
- Low-carb and gluten-free: A cozy pasta-like casserole without the noodles.
- Veggie-packed: Made with squash, mushrooms, and tomato sauce for a nourishing meal.
- Creamy & cheesy: Greek yogurt and parmesan add richness without heavy cream.
- Meal prep-friendly: Tastes even better the next day.
Ingredients & Substitutions
- Yellow Spaghetti Squash: When roasted, this squash forms tender, noodle-like strands that make a great low-carb base. You can also use cooked angel hair pasta or zucchini noodles, but the texture will differ.
- Olive Oil: Used for roasting and flavor. Avocado oil or melted butter also work well.
- Spicy Italian Sausage: Adds bold flavor and heat. Substitute with sweet Italian sausage, ground chicken, or turkey sausage for a milder version.
- White Mushrooms: Finely diced to blend into the sauce and add umami. Swap with cremini (baby bella) mushrooms or omit if you prefer.
- Yellow Onion: Adds sweetness and depth. White or red onions can be used in a pinch.
- Garlic: Fresh minced garlic offers the best flavor, but 2 1/2 teaspoons of granulated garlic works too.
- Kosher Salt: All of my recipes are tested with Morton kosher salt unless noted otherwise. It is the best salt for everyday cooking because of its size and flavor. If using table salt, the amount should be reduced. I highly recommend picking up some kosher next time you are at the store!
- Black Pepper: Adds a little bite. Feel free to use more or less depending on your preference.
- Dried Thyme: Brings an earthy, slightly minty note. Can be swapped with Italian seasoning or dried basil. You can also use one tablespoon of fresh thyme.
- Dried Oregano: A classic herb for tomato-based sauces. You can use 1 tablespoon of fresh oregano or Italian seasoning as an alternative.
- Red Chili Flakes: Adds a touch of heat. Omit for a milder dish or increase for extra spice.
- Dried Rosemary: Adds a woodsy, aromatic flavor. Crush lightly in your hand before adding to release oils. One teaspoon of fresh rosemary or thyme also works.
- Tomato Basil Pasta Sauce: A jarred shortcut that keeps things simple. Use your favorite brand or homemade marinara sauce.
- Plain Greek Yogurt: Adds creaminess and a tangy finish without heavy cream. Half a cup of sour cream or whole milk ricotta is a good substitute.
- Parmesan Reggiano: Grated for richness and umami. Pecorino Romano or Grana Padano can be used instead.
- Mozzarella Cheese: Creates that gooey, melty top layer. Part-skim or whole milk mozzarella both work well. Shredded Italian blend is another option.
- Fresh Basil: Optional, but adds a fresh, herbaceous finish. Parsley or a sprinkle of extra parmesan also work as garnishes.
Complete list of ingredients and amounts is located on the recipe card below.
How to Make Baked Spaghetti Squash Casserole
Quick Overview
- Prep squash.
- Make meat sauce.
- Sauté aromatics.
- Simmer sauce.
- Assemble casserole.
- Bake.
Step by Step Instructions
Quick Tip From Bri
Be sure to cook the mushrooms until most of the excess water evaporates. This keeps the casserole from turning watery and helps concentrate the flavor.
- Prep Squash: Preheat the oven to 400 degrees. On a baking sheet lined with parchment paper, brush all sides of the spaghetti squash with oil. Place squash halves cut-side down.
- Bake Squash & Make Meat Sauce: Bake for 40-60 minutes, or until fork tender. While the squash bakes, in a large pot over medium-high heat, cook the sausage and mushrooms. Let most of the water evaporate from the mushrooms.
- Sauté Aromatics: Add the onions, garlic, and spices. Cook for 3-4 minutes or until the onion softens.
- Simmer the Sauce: Add the sauce and simmer on medium-low heat, stirring frequently until the squash is done. The sauce should thicken up a bit.
Quick Tip From Bri
Let the spaghetti squash cool for 5–10 minutes after roasting.
- Create Spaghetti: Once the squash is done, let it cool until you can handle it. Use a fork to scrape the middle of the squash so that the spaghetti-like strands form.
- Assemble the Casserole: Fold the squash, yogurt, and parmesan cheese into the meat sauce.
- Prep for Baking: Lightly grease a 9 x 13 baking dish. Pour the squash mixture into the dish. Sprinkle the mozzarella cheese on top.
- Bake the Squash: Bake for 15 minutes, or until the edges are bubbling and the cheese is completely melted. Let stand for 5-10 minutes before serving.
Recipe Serving Suggestions
I would serve this dish with some warm bread and salad. Here are some of my favorites to create a full meal:
- Garlic Bread Rolls: These bread rolls are soft, buttery, and infused with rosemary and garlic.
- Goat Cheese Salad with Arugula: This salad is hearty and full of different textures & flavors.
- Greek Salad: Made with a herby olive oil vinaigrette dressing, this yummy salad is refreshing, light, and perfect for a healthy lunch or dinner.
Expert Tips
- Use a Large Squash: A 4-pound squash yields plenty of strands for a hearty casserole.
- Finely Dice Mushrooms: This helps them blend into the sauce and adds a meaty texture.
- Let the Squash Cool Slightly: It’ll be much easier to handle when scooping the strands.
- Don’t Skip Resting: Letting the casserole sit helps it set and makes serving cleaner.
Most Common Mistakes
- Undercooking the Squash: If it’s too firm, it won’t mix well with the sauce.
- Skipping the Mushroom Sauté: They need time to release their moisture or the sauce will be watery.
- Using Too Much Yogurt: Stick to the recipe so the sauce stays creamy, not tangy or loose.
- Not Seasoning Enough: Taste the sauce before baking and adjust salt or chili flakes as needed.
Additions & Variations
- Swap the Protein: Try ground beef, turkey, or sweet Italian sausage.
- Add Veggies: Stir in chopped spinach, kale, or bell peppers for extra nutrients.
- Extra Spice: Add a pinch of cayenne or diced jalapeño for more heat.
The 10 BEST Substitutes for Mushrooms
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Recipe FAQs
Can you make this ahead of time?
Yes, this casserole reheats great in the microwave leftover. This is one reason I prefer to use squash instead of pasta. I do not love the texture of reheated pasta but the squash holds up great.
Is spaghetti squash better for you than pasta?
Spaghetti squash is a healthier pasta alternative, as it has fewer calories and carbohydrates while providing vitamins, minerals, and fiber.
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Did you make this recipe?
If you try this recipe, please leave a star rating in the recipe card below and/or comment! I always appreciate your feedback.
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Baked Spaghetti Squash Casserole
This cheesy Spaghetti Squash Casserole is cozy, hearty, and packed with hidden veggies. It features roasted spaghetti squash, spicy Italian sausage, lots of aromatics, and a rich tomato basil sauce. It’s folded together with creamy Greek yogurt and parmesan, then topped with melty mozzarella cheese. Every bite is savory, cheesy, and comforting—but still light and nutritious.
Ingredients
- 1 large yellow spaghetti squash, about 4 pounds whole, halved & seeds removed
- 1 Tablespoon olive oil
- 1 pound ground spicy Italian sausage
- 1 8 ounce container white mushrooms, finely diced
- 1 yellow onion, diced
- 5 cloves garlic, minced*
- 1 teaspoon salt
- 5 cracked black pepper
- 1 teaspoon dried thyme
- 1 teaspoon dried oregano
- 1/2 teaspoon red chili flakes*
- 1/4 teaspoon dried rosemary
- 1 25 ounce jar tomato basil pasta sauce*
- 1/2 cup plain greek yogurt*
- 1 ounce (1/3 cup) parmesan reggiano grated
- 6 ounces (1 1/2 cups) mozzarella cheese, shredded
- fresh basil for garnishing
Instructions
- Prep Squash: Preheat the oven to 400 degrees. On a baking sheet lined with parchment paper, brush all sides of the spaghetti squash with oil. Place squash halves cut-side down.1 large yellow spaghetti squash, about 4 pounds whole, halved & seeds removed, 1 Tablespoon olive oil
- Bake Squash & Make Meat Sauce: Bake for 40-60 minutes, or until fork tender. While the squash bakes, in a large pot over medium-high heat, cook the sausage and mushrooms. Let most of the water evaporate from the mushrooms.1 pound ground spicy Italian sausage, 1 8 ounce container white mushrooms, finely diced
- Sauté Aromatics: Add the onions, garlic, and spices. Cook for 3-4 minutes or until the onion softens.1 yellow onion, diced, 5 cloves garlic, minced*, 1 teaspoon salt, 5 cracked black pepper, 1 teaspoon dried thyme, 1 teaspoon dried oregano, 1/2 teaspoon red chili flakes*, 1/4 teaspoon dried rosemary
- Simmer the Sauce: Add the sauce and simmer on medium-low heat, stirring frequently until the squash is done. The sauce should thicken up a bit.1 25 ounce jar tomato basil pasta sauce*
- Create Spaghetti: Once the squash is done, let it cool until you can handle it. Use a fork to scrape the middle of the squash so that the spaghetti-like strands form.
- Assemble the Casserole: Fold the squash, yogurt, and parmesan cheese into the meat sauce.1/2 cup plain greek yogurt*, 1 ounce (1/3 cup) parmesan reggiano
- Prep for Baking: Lightly grease a 9 x 13 baking dish. Pour the squash mixture into the dish. Sprinkle the mozzarella cheese on top.6 ounces (1 1/2 cups) mozzarella cheese, shredded
- Bake the Squash: Bake for 15 minutes, or until the edges are bubbling and the cheese is completely melted. Let stand for 5-10 minutes before serving.fresh basil for garnishing
Did you make this recipe? Leave a comment below!
Notes
- Garlic: Fresh minced garlic offers the best flavor, but 5 teaspoons of garlic paste or pre-minced garlic works too.
- Kosher Salt: All of my recipes are tested with Morton kosher salt unless noted otherwise. It is the best salt for everyday cooking because of its size and flavor. If using table salt, the amount should be reduced. I highly recommend picking up some kosher next time you are at the store!
- Red Chili Flakes: Adds a touch of heat. Omit for a milder dish or increase for extra spice.
- Tomato Basil Pasta Sauce: A jarred shortcut that keeps things simple. Use your favorite brand or homemade marinara.
- Plain Greek Yogurt: Adds creaminess and a tangy finish without heavy cream. Half a cup of sour cream or whole milk ricotta is a good substitute.
- Let the Squash Cool Slightly: It’ll be much easier to handle when scooping the strands.
- Don’t Skip Resting: Letting the casserole sit helps it set and makes serving cleaner.
Nutrition
Serving: 1serving | Calories: 511kcal | Carbohydrates: 27g | Protein: 25g | Fat: 35g | Saturated Fat: 14g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 15g | Trans Fat: 1g | Cholesterol: 84mg | Sodium: 1861mg | Fiber: 6g | Sugar: 13g
Nutrition information is automatically calculated, so should only be used as an approximation.
This is an amazing recipe: spaghetti with squash and vodka sauce. What a combination! This is absolutely delicious and the perfect comfort food recipe. Thank you for sharing!
The recipe is called vodka sauce and I don’t see any Vodka in the recipe? I’ve had pasta alla Vodka before and it has a lighter color red sauce. I’m not sure what is what? I think they have Vodka Sauce in a jar. Is that the sauce you would use for this?
Thank you!
It is my take on a “vodka sauce”. It uses Greek yogurt instead of vodka and cream to achieve a creamy tangy sauce.