This post may contain affiliate links. Please read our disclosure policy.
Spaghetti Squash Casserole with mushrooms, creamy goat cheese sauce, and crispy Parmesan topping. Enjoy this low-carb baked spaghetti squash casserole as a side dish or the main event. 
Why You’ll Love this Spaghetti Squash Casserole
If you mostly only enjoy spaghetti squash as a side dish, this casserole is the perfect way to explore its potential as a main course. The spaghetti squash’s neutral flavor makes it easy to blend with a wide range of flavors. Plus, it’s a low-carb source of fiber, as well as vitamins A and C.
The casserole filling is a savory mix of shallots, mushrooms, and garlic cooked in a creamy goat cheese sauce. Right before baking, the casserole gets topped with a crispy panko-Parmesan topping, which elevates the whole dish. You can even get a head start by roasting the spaghetti squash up to three days in advance.
Serve this baked spaghetti squash casserole as the main event, or pair it with your favorite protein. It compliments chicken, red meat (or meatless grounds), or tofu like a dream.
Recipe Ingredients and Substitutions:
- Spaghetti Squash: You need roughly 6 cups of the spaghetti-like strands from the squash flesh. This amounts to 2 small-medium sized spaghetti squashes.
- Mushrooms: For savory, umami flavor and meaty texture, baby bella (or cremini) mushrooms do the trick. You can also shiitake or sliced portobello mushrooms, if you prefer.
- Aromatics: A mix of shallots, garlic, and fresh thyme create earthy, aromatic flavor for this casserole. Alternatively, you can use chopped yellow onion here.
- Spinach: For a pop of color and extra dose of nutrients, fresh baby spinach ups the veggie ante here. You need roughly two handfuls of fresh spinach, however you can also kale or chard, if you prefer.
- Cheese: To create a creamy, delightfully tangy sauce, this recipe calls for a whole 4-oz. log of goat cheese. It’s helpful to let the cheese come close to room temperature before mixing it in the sauce. This will ensure it melts and melds effortlessly into the sauce.
- Broth + Milk: A mix of vegetable (or chicken) broth and milk are the other necessary contenders for the cream sauce. I use unsweetened almond or cashew milk, however you can also use 2% dairy or whole-milk.
- Topping: The crispy Parmesan panko topping is the crown jewel of this casserole. It’s made with 3 simple ingredients: panko breadcrumbs, grated Parmesan cheese, and just a pat of butter.
Step-by-Step Instructions:
Step 1: Bake Spaghetti Squash
Preheat oven to 375ºF. Slice the squash in half lengthwise and scoop out the seeds. Rub oil onto the flesh, or lightly coat with non-stick cooking spray. Place squash halves, flesh side-down, on a baking sheet lined with foil. For two small squashes, bake for 35 to 40 minutes. For one large squash, bake for 45 to 50 minutes, or until the flesh of the squash is easily pierced with a fork.
When cool enough to handle, pull the squash strings out of the squash’s center with a fork and transfer to a large mixing bowl. (The squash strings should resemble short strands of spaghetti.)
Step 2: Cook Mushrooms and Aromatics
In a large skillet, heat 2 Tbsp. oil over medium-high heat. Once hot, add the mushrooms and shallots; cook 6 to 7 minutes, or until soft. Next, add the garlic, red pepper flakes, and spinach; cook for 1 to 2 minutes, stirring often, until the spinach wilts down.
Step 3: Whisk in the Flour, Broth, and Milk
Whisk in the flour and cook for 2 full minutes. Next, slowly stream in the broth and milk, whisking constantly, until the liquids are fully combined. Simmer this mixture for about 5 minutes, until it starts to thicken. Season mixture with salt, pepper, and fresh thyme.
Step 4: Add Goat Cheese and Spaghetti Squash
Next, add the goat cheese and cook for 2 to 3 more minutes, stirring often, until the goat cheese melts and melds into the mixture. Once the sauce is made, add the spaghetti squash strands. Use a pair of tongs to toss the squash with the sauce until everything is well-combined.
Grease an 8×8 or 9×9 inch baking pan with non-stick cooking spray. Transfer the spaghetti squash casserole filling to the baking dish and set aside. 
Step 5: Make Panko-Parmesan Topping
Wipe the skillet clean and add a pat of butter. Once melted, add the Panko breadcrumbs and lightly toast for 3 to 5 minutes, or until slightly golden. Transfer breadcrumbs to a bowl and toss with Parmesan cheese. Sprinkle mixture over the spaghetti squash casserole.
Step 6: Bake Spaghetti Squash Casserole
Place the pan in the oven and bake for 25 to 30 minutes, or until the top is bubbly and golden. Remove from the oven and let sit for 10 minutes before serving. If desired, garnish with extra fresh thyme.
Make Ahead and Storage Tips
- To Make Ahead. Spaghetti squash can be roasted, shredded, and stored in an airtight container for up to 3 days ahead. This will save you up to an hour when you’re ready to prepare the casserole.
- To Store. Store leftovers in the refrigerator for up to 4 days.
- To Reheat. Either reheat individual portions in the microwave, or place the whole pan back in the oven at 350ºF until warmed through.
More Delicious Spaghetti Squash Recipes:
Skinny Chicken Alfredo Spaghetti Squash
Mushroom Stroganoff Spaghetti Squash
Spaghetti Squash with Vegan Vodka Sauce
Browned Butter Kale and Fontina Spaghetti Squash
If you give this baked spaghetti squash casserole a try, snap a pic and tag #dishingouthealth so I can see your beautiful creations. Also, follow along on Facebook and Pinterest for the latest recipe updates!
Spaghetti Squash Casserole with Mushrooms and Goat Cheese
Spaghetti Squash Casserole with mushrooms, creamy goat cheese sauce, and crispy Parmesan topping. Enjoy this low-carb baked spaghetti squash casserole as a side dish or the main event.
Equipment
- Large skillet
- 8x8 or 9x9 inch baking dish
Ingredients
- 6 cups spaghetti squash strands from 2 small (2 lb.) squashes or 1 large (4 lb.) squash
- 2 Tbsp. olive oil
- 8 oz. sliced cremini (baby bella) mushrooms
- 1/2 cup chopped shallots
- 1 Tbsp. minced fresh garlic
- 1/4 tsp. red pepper flakes
- 2 cups fresh baby spinach
- 3 Tbsp. all-purpose flour
- 1 cup chicken or vegetable broth
- 1 cup milk of choice (I use unsweetened cashew or almond milk)
- 1/2 tsp. kosher salt
- 1/4 tsp. black pepper
- 1 Tbsp. fresh thyme leaves
- 1 (4-oz.) log goat cheese, softened
Panko-Parmesan Topping
- 1 Tbsp. butter
- 1/2 cup plain Panko breadcrumbs
- 1/2 cup grated Parmesan cheese
Instructions
- Preheat oven to 375ºF. Slice the squash in half lengthwise and scoop out the seeds. Rub oil onto the flesh, or lightly coat with non-stick cooking spray. Place squash halves, flesh side-down, on a baking sheet lined with foil.For two small squashes, bake for 35 to 40 minutes. For one large squash, bake for 45 to 50 minutes, or until the flesh of the squash is easily pierced with a fork.When cool enough to handle, pull the squash strings out of the squash's center with a fork and transfer to a large bowl.
- In a large skillet, heat 2 Tbsp. oil over medium-high heat. Once hot, add the mushrooms and shallots; cook 6 to 7 minutes, or until soft. Add garlic, red pepper flakes, and spinach; cook 1 to 2 minutes, stirring often, until the spinach wilts down.
- Whisk in the flour and cook for 2 FULL minutes. Slowly stream in the broth and milk, whisking constantly, until the liquids are fully combined. Simmer mixture for 5 to 6 minutes, until thickened. Season with salt, pepper, and fresh thyme.
- Add the goat cheese and cook for 2 to 3 more minutes, stirring often, until the goat cheese melts and melds into the mixture. Once the sauce is smooth, add the spaghetti squash strands. Use a pair of tongs to toss squash with the sauce until everything is well-combined.
- Grease an 8x8 or 9x9 inch baking pan with non-stick cooking spray or butter. Transfer the spaghetti squash casserole filling to the baking dish and set aside.
- Wipe the skillet clean and return to medium-high heat. Add 1 Tbsp. butter. Once melted, add the Panko breadcrumbs and lightly toast for 3 to 5 minutes, or until slightly golden. (Watch closely to avoid burning.) Transfer breadcrumbs to a bowl and toss with Parmesan cheese. Sprinkle the Panko-Parmesan mixture over the spaghetti squash casserole.Bake casserole at 375ºF, uncovered, for 25 minutes, or until bubbly and golden. Remove from oven and let sit for 10 minutes before serving. Serve with extra fresh thyme, if desired.
Notes
To Make Ahead. Spaghetti squash can be roasted, shredded, and stored in an airtight container for up to 3 days ahead. This will save you up to an hour when you're ready to prepare the casserole.
To Store. Store leftovers in the refrigerator for up to 4 days.
To Reheat. Either reheat individual portions in the microwave, or place the whole pan back in the oven at 350ºF until warmed through.
Nutrition
Serving: 1.2cups | Calories: 296kcal | Carbohydrates: 26g | Protein: 14g | Fat: 17g | Saturated Fat: 5g | Sodium: 640mg | Fiber: 5g | Sugar: 6g
I calculate these values by hand to ensure accuracy, however expect up to a 10% variable depending on food brands.
If you love this recipe, please leave a star rating and review below!
Does this freeze well?
The mushrooms in this dish were amazing, picking up the flavors of the onion, garlic, and thyme. Yum! And the sauce was so good… until I added the spaghetti squash. The squash really toned down the beautiful flavors. I think next time, I’d salt and pepper the squash before roasting it, pump up the garlic, onion, and thyme, and add an extra ounce or two of goat cheese. Fun recipe!
This is such a versatile dish! It’s perfect as a main or as a side dish. Either way you choose, this dish is phenomenal and you must try it!
This recipe is amazing! I made it tonight and there was unanimous agreement that this dish is Thanksgiving side-dish worthy, and my partner stated it’s “top 5” in all the dishes I’ve ever made.
Hi Kristin, I’m so glad the recipe was a hit for you and your partner! Thank you so much for taking the time to leave a review.
My husband and I loved this! I subbed coconut flakes for the Panko breadcrumbs to lighten the gluten load. Awesome healthy tasty dish.
Hi Erin, I’m so glad the recipe was a hit for you! Thanks for taking the time to leave a rating and review.
I made this tonight and it was great. I added roasted red peppers and zucchini. I also add a bit more red chili pepper. This one’s a keeper! Thanks!
Hi Danielle – I’m so glad you enjoyed the recipe! Thank you so much for taking the time to leave a review.
I have made this twice now. It is so filling and nourishing and the red pepper flakes gives it just the slightest hint of heat. It heats up awesome for leftovers too!
I’m so glad you enjoyed it, Angie! Thank you for taking the time to leave a review!