Creamy Cheesy Spaghetti Squash Au Gratin Bake

Featured in Healthy Zucchini.

This Cheesy Spaghetti Squash Au Gratin is a comforting bake, perfect for a weeknight meal. Get the easy recipe for this delicious, cheesy dish.
Clara Rodriguez - Recipe Author
Updated on Sun Jan 11 2026 at 05:01 PM
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Creamy Cheesy Spaghetti Squash Au Gratin Bake | Natura Recipes

Honestly, I never thought I’d be a spaghetti squash person. For years, I just walked past it at the grocery store, assuming it was too much work, or worse, just bland. But then, one chilly evening, after a particularly chaotic day think spilled coffee, a missed meeting, and a dog who ate my favorite slipper I stumbled upon a recipe for a cheesy gratin. I had a lonely spaghetti squash on my counter, a gift from a neighbor's garden, and a sudden craving for something truly comforting. This dish, this amazing Cheesy Spaghetti Squash Au Gratin, became my kitchen hug. It's warm, it's gooey, and it just makes everything feel a little bit better, you know?

I remember the first time I made this Cheesy Spaghetti Squash Au Gratin, I was so focused on getting the béchamel sauce right that I completely forgot to pre-roast the squash. Oops! I ended up with a slightly crunchy, undercooked mess. Had to start all over again, which, let's be real, was a bit frustrating. But that second attempt? Oh, it was magic. The house smelled incredible, and when I pulled that bubbly, golden gratin out of the oven, I knew I had found a keeper. Sometimes the best recipes come from the biggest kitchen blunders!

Ingredients for Cheesy Spaghetti Squash Au Gratin

  • Spaghetti Squash: This is our star! It strands beautifully when cooked, mimicking pasta, which is why I love it. Look for a firm, yellow squash.
  • Unsalted Butter: We're building flavor here, so good quality butter is key. Don't skimp, honestly. It helps create that silky sauce.
  • All-Purpose Flour: Our thickening agent for the béchamel. I once tried almond flour and it worked... kinda, but the texture wasn't quite right. Stick with AP for the best results.
  • Whole Milk: For that rich, creamy sauce. Please, please, don't use skim milk, you'll lose that luxurious mouthfeel. I tried it once, and it just wasn't the same.
  • Garlic & Onion: The aromatic foundation! I always go for fresh garlic, maybe even a little extra, because, well, garlic. It adds so much depth to the Cheesy Spaghetti Squash Au Gratin.
  • Sharp Cheddar Cheese: Melts like a dream and gives that essential tangy, cheesy punch. I always grate my own, it just melts better and tastes fresher.
  • Gruyère Cheese: This is where the sophisticated flavor comes in. It has a nutty, earthy taste that elevates the gratin. If you can't find it, Swiss works as a decent substitute.
  • Nutmeg: A tiny pinch makes a huge difference in béchamel. It's that secret ingredient that gives it a warm, almost sweet undertone. Don't skip it!
  • Panko Breadcrumbs: For that irresistible crispy topping. I love how it adds a contrasting texture to the soft squash and creamy sauce.
  • Fresh Parsley: A little green for freshness and a pop of color at the end. It brightens everything up.

Making Your Cheesy Spaghetti Squash Au Gratin

Roast the Spaghetti Squash:
First things first, let's get that spaghetti squash ready. Halve it lengthwise, scoop out the seeds, and brush the cut sides with a little olive oil. Season with salt and pepper. Place cut-side down on a baking sheet and roast at 400°F (200°C) for about 30-40 minutes, or until fork-tender. This is where I always forget to season it properly, so don't be like me! You want it tender enough for the strands to pull away easily. The kitchen starts to smell faintly sweet and earthy, a promise of good things to come.
Sauté Aromatics:
While the squash is roasting, melt a couple of tablespoons of butter in a saucepan over medium heat. Add your finely diced onion and cook until it's softened and translucent, about 5-7 minutes. Then, stir in the minced garlic and cook for just another minute until fragrant. Don't let it brown, or it'll get bitter! I’ve burned garlic a few times, and trust me, it’s a sad smell. Keep an eye on it!
Build the Béchamel Sauce:
Now for the creamy magic! Sprinkle the flour over the softened onions and garlic, stirring constantly for about 1-2 minutes to cook out that raw flour taste. This is your roux, the base of our sauce. Slowly, gradually, whisk in the whole milk, a little at a time, making sure there are no lumps. Keep whisking until the sauce thickens and coats the back of a spoon. It feels like a small victory when it gets perfectly smooth!
Melt in the Cheeses:
Remove the béchamel from the heat and stir in most of your shredded sharp cheddar and Gruyère. Reserve a little for the topping, because, why not? Stir until the cheeses are completely melted and the sauce is wonderfully smooth and glossy. Season with salt, black pepper, and that tiny pinch of nutmeg. Taste it! This is your chance to adjust. I always taste here, sometimes adding a little more salt than I intended, oops!
Combine Squash and Sauce:
Once the spaghetti squash is roasted and cool enough to handle, use a fork to scrape out the strands into a large bowl. Honestly, this part is so satisfying! Pour the cheesy béchamel sauce over the squash strands and gently toss to combine everything. Make sure every strand is coated in that luscious sauce. Transfer this mixture to a greased 9x13 inch baking dish. Don't worry if it looks a little messy, that's real cooking!
Bake to Golden Perfection:
Sprinkle the remaining shredded cheeses and the Panko breadcrumbs evenly over the top of the Cheesy Spaghetti Squash Au Gratin. Pop it back into the oven at 375°F (190°C) for 20-25 minutes, or until the top is golden brown and bubbly. The smell that fills your kitchen at this point? Pure bliss! Let it rest for a few minutes before serving, then garnish with fresh parsley. It'll be piping hot and so comforting.

There's something so special about pulling this Cheesy Spaghetti Squash Au Gratin out of the oven. The bubbling cheese, the golden crust, the aroma of garlic and nutty Gruyère it just feels like home. I remember one time, my friend came over unannounced, and I had just made this. It was still warm, and we just sat at the kitchen island, eating straight from the dish with forks, laughing. Those are the moments this recipe is made for.

Storing Cheesy Spaghetti Squash Au Gratin

Leftovers of this Cheesy Spaghetti Squash Au Gratin are honestly fantastic, sometimes even better the next day as the flavors meld. Just make sure it’s completely cooled before you stash it away. I usually transfer any remaining gratin into an airtight container and pop it in the fridge. It'll keep well for about 3-4 days. I microwaved it once and the sauce separated a little so don't do that lol! Reheating gently in the oven at 300°F (150°C) for about 15-20 minutes, covered with foil, is my personal go-to. It keeps that creamy texture and prevents the top from drying out. You can also freeze individual portions for up to a month, just thaw overnight in the fridge before reheating.

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Creamy Cheesy Spaghetti Squash Au Gratin Bake - Image 1 | Natura Recipes

Cheesy Spaghetti Squash Au Gratin: Ingredient Swaps

I’ve definitely played around with substitutions for this Cheesy Spaghetti Squash Au Gratin over the years. If Gruyère isn't your jam or you can't find it, a good quality Swiss cheese or even some fontina would work beautifully. I tried mozzarella once, and it worked... kinda, but it was a bit too stringy for my preference. For the milk, if you're dairy-free, a full-fat unsweetened oat milk or cashew milk could be an option, though the sauce's richness will change a bit. You could even swap out the Panko for crushed Ritz crackers for an extra buttery, salty crunch I've done that when I was out of Panko, and it was a happy accident! Feel free to add some cooked, crumbled bacon or sautéed mushrooms to the mix for extra flavor and texture, too.

Serving Your Cheesy Spaghetti Squash Au Gratin

This Cheesy Spaghetti Squash Au Gratin is a hearty dish all on its own, but it plays well with others! For a light meal, I love serving it with a simple green salad dressed with a tangy vinaigrette. The freshness cuts through the richness of the gratin perfectly. If you're looking for something more substantial, it’s amazing alongside roasted chicken or a pan-seared pork chop. And for drinks? A crisp white wine like a Sauvignon Blanc or a light-bodied red like a Pinot Noir would be fantastic. Honestly, this dish and a rom-com on the couch? Yes please. It's the ultimate comfort meal, no matter the occasion.

Cultural Backstory of Au Gratin Dishes

The term "au gratin" comes from French cuisine, literally meaning "with a crust." It refers to any dish that's topped with breadcrumbs, cheese, or both, and then baked until a golden-brown crust forms. Think of classic potato gratins! My own connection to this style of cooking started when I lived in a small apartment in Paris during college. I was obsessed with finding simple, comforting dishes that reminded me of home, but with a French twist. While spaghetti squash isn't traditional, adapting the au gratin technique to this vegetable felt like a natural, delicious evolution. It combines that rustic, comforting French method with a modern, veggie-forward approach that I really appreciate.

Honestly, this Cheesy Spaghetti Squash Au Gratin has become a staple in my kitchen. It's a testament to how simple ingredients, a little patience, and a lot of cheese can create something truly memorable. Every time I make it, I think of that first chaotic kitchen night and how a humble squash turned into pure comfort. I hope it brings as much warmth to your table as it does to mine. Don't forget to share your versions with me!

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Creamy Cheesy Spaghetti Squash Au Gratin Bake - Image 2 | Natura Recipes

Frequently Asked Questions About Cheesy Spaghetti Squash Au Gratin

→ Can I make Cheesy Spaghetti Squash Au Gratin ahead of time?

You can definitely prep parts of it! Roast the squash and make the béchamel a day ahead. Store them separately in the fridge. Assemble and bake just before serving for the best bubbly, cheesy results. I’ve done this for dinner parties, and it saves so much stress!

→ What if I don't have Gruyère cheese for this Cheesy Spaghetti Squash Au Gratin?

No worries! A good quality Swiss cheese is a fantastic substitute, or even fontina for a slightly milder flavor. You could even use all sharp cheddar if that's what you have on hand. Don't let one ingredient stop you from making this delicious Cheesy Spaghetti Squash Au Gratin!

→ How do I get the spaghetti squash strands perfectly separated?

The trick is to roast it until it's really tender. Once it's cool enough, use a fork to gently scrape from the sides towards the center. The strands will naturally pull away. If it's still a bit firm, it needs more time in the oven.

→ Can I freeze leftover Cheesy Spaghetti Squash Au Gratin?

Yes, you can! I often freeze individual portions. Just let it cool completely, then store in an airtight, freezer-safe container for up to a month. Thaw it in the fridge overnight and reheat gently in the oven for the best texture. My kids love finding these in the freezer for a quick meal.

→ Can I add meat to this Cheesy Spaghetti Squash Au Gratin recipe?

Absolutely! Cooked ground turkey or crumbled sausage would be a delicious addition. Just brown the meat with the onions and garlic before adding the flour for the béchamel. I sometimes add some leftover shredded chicken, too, for an even heartier meal!

Creamy Cheesy Spaghetti Squash Au Gratin Bake

This Cheesy Spaghetti Squash Au Gratin is a comforting bake, perfect for a weeknight meal. Get the easy recipe for this delicious, cheesy dish.

4.3 out of 5
(10 reviews)
Prep Time
20 Minutes
Cook Time
60 Minutes
Total Time
80 Minutes

Category: Healthy Zucchini

Difficulty: Intermediate

Cuisine: American

Yield: 6 Servings

Dietary: Vegetarian

Published: Mon Nov 24 2025 at 12:27 AM

Last Updated: Sun Jan 11 2026 at 05:01 PM

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Ingredients

→ Base Ingredients

01 1 medium spaghetti squash (about 3-4 lbs)
02 2 tablespoons olive oil
03 Salt and freshly ground black pepper, to taste

→ Cheesy Béchamel Sauce

04 4 tablespoons unsalted butter
05 1/2 cup finely diced yellow onion
06 3 cloves garlic, minced
07 1/4 cup all-purpose flour
08 3 cups whole milk
09 1.5 cups shredded sharp cheddar cheese, divided
10 1 cup shredded Gruyère cheese, divided
11 1/4 teaspoon freshly grated nutmeg

→ Finishing Touches

12 1/2 cup Panko breadcrumbs
13 2 tablespoons fresh parsley, chopped

Instructions

Step 01

First things first, let's get that spaghetti squash ready. Halve it lengthwise, scoop out the seeds, and brush the cut sides with a little olive oil. Season with salt and pepper. Place cut-side down on a baking sheet and roast at 400°F (200°C) for about 30-40 minutes, or until fork-tender. This is where I always forget to season it properly, so don't be like me! You want it tender enough for the strands to pull away easily. The kitchen starts to smell faintly sweet and earthy, a promise of good things to come.

Step 02

While the squash is roasting, melt a couple of tablespoons of butter in a saucepan over medium heat. Add your finely diced onion and cook until it's softened and translucent, about 5-7 minutes. Then, stir in the minced garlic and cook for just another minute until fragrant. Don't let it brown, or it'll get bitter! I’ve burned garlic a few times, and trust me, it’s a sad smell. Keep an eye on it!

Step 03

Now for the creamy magic! Sprinkle the flour over the softened onions and garlic, stirring constantly for about 1-2 minutes to cook out that raw flour taste. This is your roux, the base of our sauce. Slowly, gradually, whisk in the whole milk, a little at a time, making sure there are no lumps. Keep whisking until the sauce thickens and coats the back of a spoon. It feels like a small victory when it gets perfectly smooth!

Step 04

Remove the béchamel from the heat and stir in most of your shredded sharp cheddar and Gruyère. Reserve a little for the topping, because, why not? Stir until the cheeses are completely melted and the sauce is wonderfully smooth and glossy. Season with salt, black pepper, and that tiny pinch of nutmeg. Taste it! This is your chance to adjust. I always taste here, sometimes adding a little more salt than I intended, oops!

Step 05

Once the spaghetti squash is roasted and cool enough to handle, use a fork to scrape out the strands into a large bowl. Honestly, this part is so satisfying! Pour the cheesy béchamel sauce over the squash strands and gently toss to combine everything. Make sure every strand is coated in that luscious sauce. Transfer this mixture to a greased 9x13 inch baking dish. Don't worry if it looks a little messy, that's real cooking!

Step 06

Sprinkle the remaining shredded cheeses and the Panko breadcrumbs evenly over the top of the Cheesy Spaghetti Squash Au Gratin. Pop it back into the oven at 375°F (190°C) for 20-25 minutes, or until the top is golden brown and bubbly. The smell that fills your kitchen at this point? Pure bliss! Let it rest for a few minutes before serving, then garnish with fresh parsley. It'll be piping hot and so comforting.

Notes

  1. Always roast your spaghetti squash until it's really tender, undercooked squash is just sad.
  2. Whisk that béchamel constantly when adding milk to avoid lumps-I've learned this the hard way!
  3. Don't be shy with the cheese on top, that golden, bubbly crust is what makes it an au gratin!
  4. For an extra layer of flavor, roast some cherry tomatoes alongside the squash and stir them in.

Tools You'll Need

  • Baking sheet
  • large saucepan
  • whisk
  • 9x13 inch baking dish

Allergy Information

Please check ingredients for potential allergens and consult a health professional if in doubt.
  • Dairy
  • Gluten

Nutrition Facts (Per Serving)

It is important to consider this information as approximate and not to use it as definitive health advice.
  • Calories: 350 Calories
  • Total Fat: 22g
  • Total Carbohydrate: 25g
  • Protein: 18g

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