If you have been craving a comforting, cheesy dish that also feels fresh and light, this Creamy Spaghetti Squash au Gratin Recipe is an absolute winner you need to try. It’s the perfect way to transform humble spaghetti squash into a rich, golden-bubbly casserole that’s loaded with layers of flavor—from tender roasted squash strands to luscious sour cream and melty Gruyère. Whether you’re looking to impress a dinner guest or just treat yourself to a cozy, gluten-free indulgence, this recipe hits all the notes of creamy, cheesy delight while keeping things wholesome and satisfying.

Ingredients You’ll Need
This Creamy Spaghetti Squash au Gratin Recipe calls for simple yet carefully chosen ingredients that work together beautifully. Each one plays a key role, from adding depth and creaminess to bringing a vibrant color and a hint of fresh aroma.
- 1 medium spaghetti squash: The star of the dish, its strands create the perfect pasta-like texture that soaks up all the creamy goodness.
- 1 tablespoon olive oil: Helps sauté the onions gently and adds a subtle fruity richness.
- 1 small onion (finely chopped): Adds sweetness and soft texture when cooked down.
- 2 cloves garlic (minced): Brings a warm, savory punch without overpowering the dish.
- ½ cup sour cream: Provides that luscious, creamy base essential for the au gratin’s velvety texture.
- ½ cup grated Parmesan cheese: Offers sharp, nutty flavor and a wonderful savory backbone.
- 1 cup shredded Gruyère or cheddar cheese (divided): Gruyère melts beautifully for a smooth topping, while cheddar adds a delicious tangy bite.
- ½ teaspoon salt: Enhances all the natural flavors.
- ¼ teaspoon black pepper: Adds just the right subtle heat to balance the creaminess.
- ¼ teaspoon dried thyme (optional): A delicate herbal note that elevates the flavor profile.
- Chopped parsley for garnish (optional): Offers a fresh, bright finish and a pop of color.
How to Make Creamy Spaghetti Squash au Gratin Recipe
Step 1: Roast the Spaghetti Squash
Start by preheating your oven to 400°F. Cut the squash in half lengthwise and scoop out the seeds—this helps it cook evenly. Place the halves cut-side down on a parchment-lined baking sheet to roast for about 35 to 40 minutes. When it’s tender and gives easily to a fork, let it cool slightly before scraping out the delicious squash strands. This roasting step brings out a subtle sweetness and helps the squash perfectly absorb those creamy flavors later on.
Step 2: Sauté Onion and Garlic
While the squash roasts, heat olive oil in a skillet over medium heat. Add your finely chopped onion and let it cook gently for 4 to 5 minutes until it’s soft and translucent—this mellowed sweetness is key. Toss in the minced garlic and sauté for just 30 more seconds, releasing that irresistible aroma that makes your kitchen feel warm and inviting.
Step 3: Combine the Ingredients
In a large mixing bowl, bring together the roasted spaghetti squash strands, sautéed onion and garlic, creamy sour cream, sharp Parmesan, and half of your shredded Gruyère or cheddar. Season with salt, pepper, and thyme if you’re using it. Stir everything until the cheese starts to mingle with the creamy base, ensuring every strand is coated with flavor.
Step 4: Bake to Golden Perfection
Transfer this beautiful mixture into a greased 8×8-inch baking dish and sprinkle the remaining cheese on top for a melty, golden crust. Lower your oven temperature to 375°F and bake it for 20 to 25 minutes until the casserole is bubbly and irresistibly golden brown. For an extra touch, you can broil it for 1 to 2 minutes at the end to get that perfectly browned, slightly crisp top – pure magic!
How to Serve Creamy Spaghetti Squash au Gratin Recipe

Garnishes
To make your Creamy Spaghetti Squash au Gratin Recipe look even more inviting, sprinkle freshly chopped parsley right before serving. This little green sprinkle adds a fresh, slightly peppery lift and enhances the vibrant color, making your dish look as good as it tastes.
Side Dishes
This au gratin pairs wonderfully with a crisp green salad tossed in lemon vinaigrette or roasted veggies like asparagus or Brussels sprouts. If you want to keep things hearty, grilled chicken or a simple pan-seared fish complements the creamy squash perfectly, turning it into a balanced, memorable meal.
Creative Ways to Present
For a fun twist, serve this creamy gratin in individual ramekins or use hollowed-out spaghetti squash shells as natural bowls. It’s an impressive way to present the dish when entertaining and keeps every bite warm and cozy from oven to table.
Make Ahead and Storage
Storing Leftovers
Leftover Creamy Spaghetti Squash au Gratin Recipe stores beautifully in an airtight container in the refrigerator for up to 3 days. The flavors deepen overnight, so the next day it’s even tastier!
Freezing
To freeze, let the dish cool completely, then transfer it to a freezer-safe container. It keeps well for up to 2 months. Thaw overnight in the fridge before reheating to preserve texture and flavor.
Reheating
Reheat leftovers in the oven at 350°F until warmed through to restore that creamy, melted magic. If you’re short on time, a microwave works too—just cover loosely and heat in short bursts to avoid drying out the dish.
FAQs
Can I use another type of cheese instead of Gruyère or cheddar?
Absolutely! Swiss or mozzarella are great melty options. If you prefer a sharper flavor, aged gouda also works wonderfully. Just choose cheeses that melt well for that signature au gratin creaminess.
Is this dish gluten-free?
Yes, this Creamy Spaghetti Squash au Gratin Recipe is naturally gluten-free as it uses spaghetti squash instead of pasta, making it a great option for anyone avoiding gluten.
Can I make this recipe vegan?
You can! Swap sour cream for a plant-based alternative, and use vegan cheeses that melt well. Just keep in mind the flavors and textures might shift slightly, but it will still be delicious.
How can I add protein to this dish?
Adding cooked bacon bits, diced rotisserie chicken, or even sautéed mushrooms makes this dish more filling while maintaining its creamy, comforting appeal.
What if I don’t have fresh parsley for garnish?
No worries! You can use dried parsley, chopped chives, or even a sprinkle of fresh thyme to add a hint of color and bite on top.
Final Thoughts
I cannot recommend enough giving this Creamy Spaghetti Squash au Gratin Recipe a spot in your regular rotation. It’s that rare gem of a dish that feels indulgent yet light, elegant yet simple. Every bite brings warmth and satisfaction, with layers of flavor that make it a new favorite for family dinners or special occasions. So grab a squash, invite some cheese over, and treat yourself to this unforgettable creamy delight.
Print
Creamy Spaghetti Squash au Gratin Recipe
- Prep Time: 15 minutes
- Cook Time: 1 hour
- Total Time: 1 hour 15 minutes
- Yield: 4–6 servings
- Category: Side Dish
- Method: Baking
- Cuisine: American
- Diet: Vegetarian, Gluten Free
Description
Creamy Spaghetti Squash au Gratin is a delicious and comforting low-carb side dish featuring roasted spaghetti squash mixed with sautéed onions, garlic, sour cream, Parmesan, and Gruyère cheese, baked to golden bubbly perfection.
Ingredients
Vegetables
- 1 medium spaghetti squash (about 2½–3 pounds)
- 1 small onion, finely chopped
- 2 cloves garlic, minced
- Chopped parsley for garnish (optional)
Dairy & Oils
- 1 tablespoon olive oil
- ½ cup sour cream
- ½ cup grated Parmesan cheese
- 1 cup shredded Gruyère or cheddar cheese, divided
Seasonings
- ½ teaspoon salt
- ¼ teaspoon black pepper
- ¼ teaspoon dried thyme (optional)
Instructions
- Preheat and Roast Squash: Preheat your oven to 400°F. Cut the spaghetti squash in half lengthwise and scoop out the seeds. Place the halves cut-side down on a parchment-lined baking sheet and roast for 35–40 minutes until the flesh is tender. Allow to cool slightly, then use a fork to scrape out the squash strands into a large bowl.
- Sauté Aromatics: While the squash roasts, heat the olive oil in a skillet over medium heat. Add the finely chopped onion and sauté for 4–5 minutes until softened. Add the minced garlic and cook for an additional 30 seconds until fragrant.
- Mix Ingredients: To the bowl with the spaghetti squash strands, add the sautéed onion and garlic, sour cream, grated Parmesan, half of the shredded Gruyère or cheddar cheese, salt, black pepper, and dried thyme if using. Stir until all the ingredients are well combined.
- Assemble and Bake: Grease an 8×8-inch baking dish and transfer the squash mixture into it evenly. Sprinkle the remaining shredded cheese on top. Bake at 375°F for 20–25 minutes, until the casserole is bubbly and the top is golden brown. For extra browning, broil for 1–2 minutes at the end if desired.
- Garnish and Serve: Remove from oven and let cool slightly. Garnish with chopped parsley if using, then serve warm as a comforting side dish or light main.
Notes
- This dish is a great low-carb, gluten-free side and works well as a vegetarian main course.
- For added protein, stir in cooked bacon pieces or shredded rotisserie chicken before baking.
- To get a crispier top, use the broil function carefully and watch closely to prevent burning.
- Use either Gruyère or cheddar cheese based on your preference; both melt beautifully.

