As I stood in my kitchen, the aroma of sautéed garlic and onions filled the air, instantly whisking me away to comforting family dinners of my childhood. Today, I’m excited to share my spin on a classic dish with this Creamy Spaghetti Squash Au Gratin. This healthy and gluten-free alternative to mac and cheese not only satisfies cravings but also provides a nourishing boost thanks to the tender, sweet spaghetti squash. It’s the perfect weeknight dinner that feels indulgent yet is packed with nutrients, making it a guilt-free comfort food. Plus, it’s incredibly easy to customize—whether you want to sneak in some sautéed veggies or add a protein twist, the options are endless! Curious to find out how to create a meal that transforms an ordinary squash into a gourmet dish? Let’s dive in!

Why is Spaghetti Squash Au Gratin Amazing?
Healthy Twist: This dish offers a nutritious alternative to traditional mac and cheese, satisfying your cravings without the guilt.
Customizable Goodness: Add proteins like chicken or crumbled sausage, or even sneak in some sautéed veggies to boost flavor and nutrition.
Simple Preparation: With straightforward steps, preparing this dish can be a breeze, making it perfect for busy weeknights.
Crowd-Pleaser: Whether for family gatherings or casual dinners, this creamy treat is sure to wow everyone at the table, even picky eaters!
Imagine serving this alongside a fresh salad or grilled meat for a complete meal, just like you would with my Creamy Spaghetti and Meatballs Warm or Omas Easy German Spaghetti recipes. Your loved ones will be raving about it!
Spaghetti Squash Au Gratin Ingredients
For the Squash
• Spaghetti Squash – The star of this dish, offering a light and slightly sweet flavor that mimics pasta beautifully.
• Unsalted Butter – Adds a rich, creamy base to the cheese sauce; olive oil can be used for a dairy-free option.
For the Cheese Sauce
• Yellow Onion – Provides a natural sweetness and depth when sautéed, making the sauce more flavorful.
• Garlic – A must-have for enhancing the overall flavor with its delightful aroma.
• All-Purpose Flour – Thickens the cheese sauce for a luscious consistency; swap with gluten-free flour for a gluten-free adaptation.
• Whole Milk – Gives the sauce a creamy texture; low-fat milk or a dairy-free alternative works just as well.
• Salt, Black Pepper, Nutmeg – Key seasonings to elevate the flavors of your sauce.
For the Cheesy Layer
• Gruyere Cheese – Melts beautifully and adds a nutty flavor; Swiss cheese can be substituted for a similar taste.
• Sharp Cheddar Cheese – Contributes vibrant color and a sharp flavor that complements the dish perfectly.
• Parmesan Cheese – Provides a salty finish and umami depth that enhances the overall flavor profile.
For the Crunchy Topping
• Panko Breadcrumbs – Ensures a delightful crunchy topping, creating a lovely contrast to the creamy filling.
• Fresh Parsley – Optional garnish to add a pop of color and freshness to your plated dish.
This Spaghetti Squash Au Gratin will not only delight your taste buds but also showcase how healthy ingredients can transform a classic comfort food into a guilt-free delight!
Step‑by‑Step Instructions for Spaghetti Squash Au Gratin
Step 1: Preheat the Oven
Begin by preheating your oven to 400°F (200°C). This step ensures a perfectly cooked Spaghetti Squash Au Gratin with a beautifully browned top. Don’t forget to arrange your oven rack in the center to allow for even cooking as your squash roasts later on.
Step 2: Prepare the Spaghetti Squash
Carefully slice the spaghetti squash in half lengthwise and scoop out its seeds using a spoon. Next, place the squash cut-side up on a baking sheet. Season the insides with a generous coating of unsalted butter, salt, and pepper, inviting a depth of flavor that will blend wonderfully with the cheese sauce later.
Step 3: Roast the Squash
Roast the squash in your preheated oven for 45-60 minutes, or until the flesh is tender and easily pierced with a fork. Keep an eye on it towards the end; the golden edges and soft texture are indicators that your spaghetti squash is ready to be transformed into a creamy dish!
Step 4: Shred the Squash
Once the squash has cooled enough to handle, use a fork to gently rake the flesh into strands that resemble spaghetti. This step will give your Spaghetti Squash Au Gratin its signature texture. Set aside the shredded strands as we move on to prepare the cheesy goodness.
Step 5: Sauté the Aromatics
In a medium saucepan, melt the remaining unsalted butter over medium heat. Add diced yellow onion and cook for about 5 minutes, stirring until they turn translucent. Then, add minced garlic and sauté for just a minute more, letting those rich aromas fill your kitchen—this is the fragrant foundation for your cheese sauce!
Step 6: Make the Roux
Sprinkle all-purpose flour into the saucepan and whisk it together, cooking for 1-2 minutes until lightly golden. This roux thickens the cheese sauce for your Spaghetti Squash Au Gratin, creating a luscious texture. The mixture should bubble slightly, indicating it’s ready for the next step.
Step 7: Create the Cheese Sauce
Slowly whisk in whole milk while maintaining medium heat. Continue stirring until the sauce thickens and begins to bubble, about 3-5 minutes. The goal is a smooth, creamy consistency that will envelop the spaghetti squash in rich, cheesy deliciousness.
Step 8: Add Seasonings and Cheese
Season the sauce with salt, black pepper, and a pinch of nutmeg. After that, stir in the Gruyere, sharp cheddar, and Parmesan cheese, watching as they melt into the creamy base, forming a flavor-packed sauce. This is the moment when your Spaghetti Squash Au Gratin starts to shine!
Step 9: Combine the Squash and Sauce
Fold the shredded spaghetti squash gently into the cheese sauce until well combined. Ensure every strand is coated in the creamy mixture, allowing the flavors to meld beautifully. This golden blend deserves to shine when baked to perfection!
Step 10: Prepare for Baking
Transfer your cheesy spaghetti squash mixture into a greased baking dish, spreading it evenly. This is the home for your soon-to-be-baked creation! Top with a sprinkle of panko breadcrumbs and additional cheese for that irresistible crunchy layer that contrasts perfectly with the creamy filling.
Step 11: Bake to Perfection
Place the baking dish into the oven and bake for 20-25 minutes, or until the topping is golden and crispy. Keep an eye on it towards the end, as the smell of bubbling cheese will make it hard to wait!
Step 12: Cool and Serve
Once out of the oven, let your Spaghetti Squash Au Gratin cool for 5-10 minutes. This brief moment allows the dish to set, making it easier to serve. Before plating, garnish with fresh parsley for a pop of color to brighten your delightful bowl of comfort!

Spaghetti Squash Au Gratin Variations
Feel free to mix and match these suggestions to make this dish truly your own!
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Dairy-Free: Use unsweetened almond milk and dairy-free cheese to create a creamy sauce without the dairy.
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Gluten-Free: Substitute all-purpose flour with a gluten-free blend to keep the dish friendly for gluten-sensitive diners.
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Protein-Packed: Toss in shredded rotisserie chicken or Italian sausage for a heartier meal that’s still delicious.
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Veggie Boost: Add sautéed spinach, bell peppers, or zucchini to enhance nutritional value and add irresistible flavors.
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Cheesy Experiment: Swap out Gruyere for Fontina or Havarti cheese for a unique twist on the traditional flavors!
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Spice It Up: Incorporate some chopped jalapeños or a pinch of cayenne pepper into the cheese sauce for an extra kick.
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Nutty Crunch: For a different topping texture, consider using crushed nuts, such as walnuts or pecans, along with panko for a delightful crunch.
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Herbaceous Touch: Experiment with fresh herbs like thyme or rosemary to elevate the flavor profile and add a fragrant note reminiscent of Italian cuisine.
You can also explore comforting alternatives like my Garlic Butter Squash and enjoy the flavor of Spaghetti Meatballs Warm for meal inspirations that could complement your Spaghetti Squash Au Gratin!
Make Ahead Options
These Spaghetti Squash Au Gratin are perfect for busy weeknights! You can roast the spaghetti squash and prepare the cheese sauce up to 24 hours in advance. Simply store the squash strands and cheese sauce separately in airtight containers in the refrigerator to preserve their freshness and quality. Additionally, you can fully assemble the dish (excluding the breadcrumbs) and refrigerate it for up to 3 days before baking. When it’s time to serve, just sprinkle the panko topping on, then bake it directly from the fridge, adding a few extra minutes to the baking time. This way, you’ll have a creamy, delicious meal with minimal effort when you’re ready to eat!
What to Serve with Spaghetti Squash Au Gratin
Create a delightful meal that enhances the creamy comfort of your dish while adding fresh flavors and textures.
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Grilled Chicken: This protein-packed addition balances the creamy richness of the gratin and adds a healthy, filling component.
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Mixed Greens Salad: A light, crunchy salad with a zesty vinaigrette cuts through the richness, providing a refreshing contrast to the au gratin.
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Roasted Brussels Sprouts: Their nutty flavor and crispy edges complement the creaminess beautifully, adding a touch of heartiness to your table.
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Garlic Bread: Who can resist warm, buttery garlic bread? It’s perfect for savoring every drop of the cheesy sauce.
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Steamed Asparagus: The bright, grassy flavor of asparagus elevates the dish, offering a lovely textural and visual contrast.
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Herb-Infused Quinoa: This nutrient-rich side adds a nutty flavor that pairs well with the creamy flavors of the gratin while boosting your fiber intake.
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Chardonnay: A chilled glass of Chardonnay enhances the cheese’s flavor profile, making every bite of your Spaghetti Squash Au Gratin even more enjoyable.
How to Store and Freeze Spaghetti Squash Au Gratin
Fridge: Store leftovers in an airtight container for up to 3-4 days. Reheat in the oven at 350°F (175°C) until warmed through for best results.
Freezer: For longer storage, freeze portions in airtight containers or freezer bags for up to 2 months. Thaw in the fridge before reheating.
Reheating: To revive your Spaghetti Squash Au Gratin, reheat in the oven at 350°F (175°C) for about 20 minutes, or microwave until hot.
Assembly Tip: You can assemble the dish ahead of time, cover tightly, and refrigerate overnight. Bake as instructed when ready to enjoy!
Expert Tips for Spaghetti Squash Au Gratin
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Choose the Right Squash: Opt for a spaghetti squash that feels heavy for its size; this ensures a sweeter, more flavorful dish while preventing excess moisture.
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Perfect Cheese Sauce: Use high-quality cheeses like Gruyere and sharp cheddar for maximum flavor impact. Avoid overcooking the sauce to keep it creamy and smooth.
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Batch Cooking: This Spaghetti Squash Au Gratin can be assembled ahead of time! Prep it in advance and refrigerate, adding a few extra minutes to baking time if cold.
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Enhance Flavors: For a little zing, blend in red pepper flakes or a dash of mustard powder into the cheese sauce. This will elevate the overall taste beautifully.
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Texture Matters: Watch the baking time closely to achieve a golden, crunchy topping. Underbaking can leave the topping soft, while overbaking may burn it.

Spaghetti Squash Au Gratin Recipe FAQs
What should I look for when selecting a spaghetti squash?
Choose a spaghetti squash that feels heavy for its size and has a firm, smooth rind. Avoid any with dark spots or blemishes, as these can indicate overripeness or spoilage. A good squash should feel solid, and the color should be vibrant.
How should I store leftover Spaghetti Squash Au Gratin?
Store any leftovers in an airtight container in the refrigerator for up to 3-4 days. When you’re ready to enjoy, reheat it in the oven at 350°F (175°C) until warmed through, which typically takes about 20 minutes, depending on your portion size.
Can I freeze Spaghetti Squash Au Gratin?
Absolutely! You can freeze portions in airtight containers or freezer bags for up to 2 months. To thaw, simply move it to the fridge overnight. Reheat in the oven at 350°F (175°C) for about 20-25 minutes, or until it’s heated through and bubbly.
What can I do if my cheese sauce isn’t thickening?
If your cheese sauce isn’t thickening, it may be due to insufficient cooking time of the roux. Make sure you let the flour cook with the butter for at least 1-2 minutes before adding the milk. If it’s still runny after adding the milk, continue to simmer it, stirring frequently. If needed, you can whisk in a bit more flour; just be sure to let it cook for another minute before adding more cheese.
Is Spaghetti Squash Au Gratin safe for people with dietary restrictions?
This recipe can be modified to fit various dietary needs. It’s gluten-free if you substitute the all-purpose flour with a gluten-free alternative. For dairy-free options, use olive oil instead of butter and a non-dairy milk along with vegan cheese. Always check the specific cheese for animal rennet if you’re concerned about vegetarian options.
Can I prepare Spaghetti Squash Au Gratin in advance?
Yes! You can assemble the dish ahead of time, cover it tightly with plastic wrap or foil, and refrigerate it overnight. This makes it a fantastic make-ahead meal! When you’re ready to bake it, just add a few extra minutes to the cooking time since it will be coming from the fridge.

Creamy Spaghetti Squash Au Gratin
Ingredients
Equipment
Method
- Preheat your oven to 400°F (200°C).
- Slice the spaghetti squash in half lengthwise and scoop out the seeds. Season with unsalted butter, salt, and pepper.
- Roast the squash for 45-60 minutes until tender.
- Once cooled, shred the squash into strands.
- Melt remaining butter in a saucepan, sauté onions for 5 minutes, add garlic for 1 minute.
- Sprinkle in the flour, whisking for 1-2 minutes until golden.
- Slowly whisk in the milk and cook until thickened, about 3-5 minutes.
- Add seasonings, then stir in the cheeses until melted.
- Fold the shredded squash into the cheese sauce until well combined.
- Transfer to a greased baking dish, top with panko and extra cheese.
- Bake for 20-25 minutes until topping is golden.
- Let cool for 5-10 minutes before serving, garnish with parsley.
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