Creamy Cheesy Spaghetti Squash Au Gratin Bake

Featured in Hearty Main Dishes.

Experience a comforting Cheesy Spaghetti Squash Au Gratin. This hearty bake, full of rich flavors, makes a satisfying, wholesome meal.
Isabella rossi
Updated on Mon Nov 24 2025 at 12:17 AM
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Honestly, this cheesy Spaghetti Squash Au Gratin wasn't a recipe I set out to create. My kitchen, usually a place of controlled chaos, had a moment. I was trying to recreate a fancy gratin I'd had at a little bistro, but with a healthier twist. Spaghetti squash was just sitting there, looking all innocent, and I thought, "Why not?" I didn't expect it to become this rich, bubbly, unbelievably satisfying dish that now cures all my comfort food cravings. The smell of the roasting squash and melting cheese just fills the house, and it feels like a warm hug, even when I've accidentally splattered cheese sauce all over the counter.

I remember one time, I was so excited to get this Cheesy Spaghetti Squash Au Gratin into the oven that I completely forgot to add the nutmeg to the cheese sauce. Oops! Halfway through baking, I realized it, but you know what? It still tasted amazing. A little less 'fancy bistro,' maybe, but still delicious. It just goes to show, sometimes kitchen mishaps lead to happy discoveries, or at least, a good laugh.

Ingredients for Cheesy Spaghetti Squash Au Gratin

  • Spaghetti Squash: This is our star, obviously! It gives you that lovely pasta-like texture without the actual pasta. I usually go for a medium-sized one, about 3 pounds.
  • Unsalted Butter: For sautéing and making that rich roux. Honestly, good butter makes all the difference here, don't skimp on it.
  • All-Purpose Flour: Our secret weapon for a thick, luscious sauce. I tried once with cornstarch, and it just wasn't the same. Stick to flour for that classic béchamel feel.
  • Whole Milk: Don't even think about skim milk, just don't. Whole milk gives us that creamy, dreamy texture that makes this Cheesy Spaghetti Squash Au Gratin so decadent.
  • Sharp Cheddar Cheese: Freshly grated, always! The pre-shredded stuff has additives and just doesn't melt the same. I once used pre-shredded and it was clumpy, total disaster.
  • Gruyère Cheese: This is where the magic happens for that classic au gratin flavor. It adds a nutty, complex note. If you can't find it, a good Swiss will do, but Gruyère is king.
  • Garlic Powder: A little goes a long way to add depth. I love garlic, so sometimes I add a tiny bit more than the recipe calls for, shhh!
  • Onion Powder: Similar to garlic powder, it just rounds out the savory notes.
  • Nutmeg: This is what makes a béchamel sing! It’s subtle but essential. I honestly forget it sometimes, but when it's there, oh, it's a game-changer.
  • Salt & Freshly Ground Black Pepper: Season to taste, of course. I always taste as I go, it’s a must for any good cook.
  • Panko Breadcrumbs: For that irresistible crispy topping. I love the extra crunch it adds!

Crafting Your Cheesy Spaghetti Squash Au Gratin

Prep the Squash:
First things first, let's get that spaghetti squash ready! I usually preheat my oven to 400°F (200°C). Then, carefully, and I mean carefully because these things can be tricky, cut your squash in half lengthwise. Scoop out all those seeds and stringy bits. A big spoon works great for this. Drizzle the cut sides with a little olive oil, salt, and pepper. Place them cut-side down on a baking sheet. Roast for about 40-50 minutes, or until you can easily pierce the skin with a fork. Honestly, don't rush this part, perfectly tender squash is key!
Shred the Squash:
Once the squash is cool enough to handle, grab a fork and start scraping the flesh away from the skin. It'll come out in those lovely spaghetti-like strands, hence the name! This is where I sometimes get a little messy, with strands flying everywhere, but it's part of the fun, right? Place all those beautiful strands into a large bowl. You want about 6-7 cups of cooked squash. If you have extra, save it for another meal!
Make the Roux:
Now for the cheese sauce, the heart of our Cheesy Spaghetti Squash Au Gratin! In a large saucepan or Dutch oven, melt the butter over medium heat. Once it's bubbly, whisk in the flour. Stir constantly for about 1-2 minutes until it forms a pale, golden paste. This is your roux, and it'll smell a little nutty, which is a good sign! Don't let it burn, though, a burnt roux is a sad roux.
Build the Sauce:
Gradually, and I mean gradually, whisk in the whole milk to your roux. Start with a small amount, whisk until smooth, then add more. This prevents lumps, and trust me, you don't want a lumpy cheese sauce! Bring the mixture to a gentle simmer, whisking occasionally, until it thickens. It should coat the back of a spoon nicely. This usually takes about 5-7 minutes. It'll start to feel velvety, and that's when you know you're on the right track.
Melt the Cheeses:
Remove the saucepan from the heat. Stir in the sharp cheddar and Gruyère cheeses until they're completely melted and the sauce is smooth and glossy. This is where the magic happens, and the sauce transforms into that rich, cheesy goodness. Season with garlic powder, onion powder, nutmeg, salt, and pepper. Taste it! Does it need more salt? A little more pepper? Make it yours! I always taste here and sometimes add a pinch more garlic powder because I'm a garlic fiend.
Assemble and Bake:
Pour the glorious cheese sauce over your spaghetti squash strands in the large bowl. Gently toss to combine, making sure every strand is coated in that cheesy goodness. Transfer the mixture to a 9x13 inch baking dish. Sprinkle the panko breadcrumbs evenly over the top. Bake for 20-25 minutes, or until the topping is golden brown and bubbly. It should smell absolutely divine, like pure comfort. Let it rest for a few minutes before serving, honestly, it's hard to wait, but it helps it set!

There's something so satisfying about pulling this Cheesy Spaghetti Squash Au Gratin out of the oven, all bubbly and golden. It always reminds me of those chilly evenings when you just need something hearty and warm. Once, I had a friend over, and she swore it was actual pasta! I didn't correct her right away, it was too funny. The kitchen might be a bit of a mess afterward, but that's just proof of a good meal, right?

Storing Cheesy Spaghetti Squash Au Gratin

This Cheesy Spaghetti Squash Au Gratin is honestly fantastic for leftovers, which is a huge win in my book! Once it's completely cooled down, just pop it into an airtight container. It keeps beautifully in the fridge for up to 3-4 days. I've found that reheating it gently in the oven at around 300°F (150°C) for about 20 minutes works best to keep that lovely texture and prevent the sauce from separating. Microwaving is okay in a pinch, but sometimes the sauce can get a little watery, so I try to avoid it if I can. It also freezes pretty well! Just portion it out, wrap it tightly, and freeze for up to 2 months. Thaw overnight in the fridge before reheating.

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Cheesy Spaghetti Squash Au Gratin Ingredient Substitutions

Life happens, and sometimes you don't have exactly what the recipe calls for. For the cheese, I've tried using a mix of mozzarella and Parmesan instead of Gruyère, and it worked... kinda. It was still tasty, but lacked that specific nutty depth. If you don't have sharp cheddar, a good Monterey Jack or even a colby jack would be decent. For the milk, if you're out of whole milk, 2% will do, but you might lose a little creaminess, just to be real. If you're looking for a gluten-free option, you can swap the all-purpose flour for a 1:1 gluten-free flour blend in the roux. I've done it, and it works surprisingly well! Just make sure to whisk extra diligently to avoid any lumps.

Cheesy Spaghetti Squash Au Gratin Serving Suggestions

This Cheesy Spaghetti Squash Au Gratin is a hearty meal all on its own, but it loves a good companion! I often serve it with a simple, crisp green salad with a light vinaigrette, the tanginess cuts through the richness beautifully. A side of roasted broccoli or asparagus also pairs wonderfully, adding some freshness and extra veggies. For drinks, a dry white wine, like a Sauvignon Blanc, is a lovely match, or even just a sparkling water with a lemon wedge. And for dessert? Something light, like a fruit tart or a scoop of sorbet, would be just right. This dish and a good movie? Yes please! It’s perfect for a cozy, relaxed evening.

A Little Story Behind This Au Gratin

While Cheesy Spaghetti Squash Au Gratin isn't some ancient family recipe passed down for generations, it has become a staple in my kitchen, carrying its own little history. The concept of 'au gratin' itself is wonderfully French, meaning 'with a crust,' often of breadcrumbs and cheese, baked until golden. It speaks to comfort and simple elegance. My personal connection started with that accidental substitution of spaghetti squash for potatoes. It felt like a culinary rebellion that turned out to be incredibly delicious and, honestly, a lot lighter. It became my go-to for using up that lone spaghetti squash on the counter, transforming it into something truly special and comforting for my little family.

So, there you have it, my Cheesy Spaghetti Squash Au Gratin. It’s a dish born from a little kitchen improvisation and a lot of love for cheesy, bubbly goodness. It always turns out so satisfying, with that golden crust and creamy interior. I hope it brings as much warmth and comfort to your table as it does to mine. Don't be shy about making it your own, and if you try it, let me know how it goes! Happy cooking, friend!

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Frequently Asked Questions

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

Absolutely! You can assemble the entire dish, minus the breadcrumbs, and refrigerate it for up to 24 hours. Add the breadcrumbs right before baking for the best crunch. It’s a lifesaver for busy evenings!

→ What if I don't have Gruyère cheese?

No worries! A good quality Swiss cheese or even a sharp white cheddar can work as a substitute. The flavor profile will be a bit different, but it'll still be wonderfully cheesy and delicious, I promise!

→ My cheese sauce is lumpy, what did I do wrong?

Oh, I've been there! Usually, it means the milk was added too quickly. Just keep whisking vigorously over low heat. If it’s really lumpy, you can try passing it through a fine-mesh sieve, a trick I learned from a minor kitchen disaster.

→ How do I store leftover Cheesy Spaghetti Squash Au Gratin?

Once cooled, transfer any leftovers to an airtight container and refrigerate for up to 3-4 days. Reheat gently in the oven for the best texture, the microwave can make it a little watery, which I found out the hard way!

→ Can I add other vegetables to this dish?

Totally! Sautéed spinach, mushrooms, or even some finely diced bell peppers would be lovely additions. I once threw in some leftover roasted broccoli, and it was a surprisingly good touch. Experiment away!

Creamy Cheesy Spaghetti Squash Au Gratin Bake

Experience a comforting Cheesy Spaghetti Squash Au Gratin. This hearty bake, full of rich flavors, makes a satisfying, wholesome meal.

4.3 out of 5
(82 reviews)
Prep Time
25 Minutes
Cook Time
65 Minutes
Total Time
90 Minutes

Category: Hearty Main Dishes

Difficulty: Intermediate

Cuisine: American

Yield: 6 Servings

Dietary: Vegetarian

Published: Mon Nov 24 2025 at 12:17 AM

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Ingredients

→ Base Ingredients

01 1 medium spaghetti squash (about 3 lbs)
02 3 tbsp unsalted butter
03 3 tbsp all-purpose flour
04 3 cups whole milk

→ Cheesy Goodness

05 1 ½ cups shredded sharp cheddar cheese, freshly grated
06 1 cup shredded Gruyère cheese, freshly grated

→ Flavor Boosters

07 1 tsp garlic powder
08 ½ tsp onion powder
09 ¼ tsp freshly grated nutmeg
10 Salt and freshly ground black pepper, to taste

→ Crunchy Topping

11 ½ cup panko breadcrumbs

Instructions

Step 01

First things first, let's get that spaghetti squash ready! I usually preheat my oven to 400°F (200°C). Then, carefully, and I mean *carefully* because these things can be tricky, cut your squash in half lengthwise. Scoop out all those seeds and stringy bits. A big spoon works great for this. Drizzle the cut sides with a little olive oil, salt, and pepper. Place them cut-side down on a baking sheet. Roast for about 40-50 minutes, or until you can easily pierce the skin with a fork. Honestly, don't rush this part, perfectly tender squash is key!

Step 02

Once the squash is cool enough to handle, grab a fork and start scraping the flesh away from the skin. It'll come out in those lovely spaghetti-like strands, hence the name! This is where I sometimes get a little messy, with strands flying everywhere, but it's part of the fun, right? Place all those beautiful strands into a large bowl. You want about 6-7 cups of cooked squash. If you have extra, save it for another meal!

Step 03

Now for the cheese sauce, the heart of our Cheesy Spaghetti Squash Au Gratin! In a large saucepan or Dutch oven, melt the butter over medium heat. Once it's bubbly, whisk in the flour. Stir constantly for about 1-2 minutes until it forms a pale, golden paste. This is your roux, and it'll smell a little nutty, which is a good sign! Don't let it burn, though, a burnt roux is a sad roux.

Step 04

Gradually, and I mean gradually, whisk in the whole milk to your roux. Start with a small amount, whisk until smooth, then add more. This prevents lumps, and trust me, you don't want a lumpy cheese sauce! Bring the mixture to a gentle simmer, whisking occasionally, until it thickens. It should coat the back of a spoon nicely. This usually takes about 5-7 minutes. It'll start to feel velvety, and that's when you know you're on the right track.

Step 05

Remove the saucepan from the heat. Stir in the sharp cheddar and Gruyère cheeses until they're completely melted and the sauce is smooth and glossy. This is where the magic happens, and the sauce transforms into that rich, cheesy goodness. Season with garlic powder, onion powder, nutmeg, salt, and pepper. Taste it! Does it need more salt? A little more pepper? Make it yours! I always taste here and sometimes add a pinch more garlic powder because I'm a garlic fiend.

Step 06

Pour the glorious cheese sauce over your spaghetti squash strands in the large bowl. Gently toss to combine, making sure every strand is coated in that cheesy goodness. Transfer the mixture to a 9x13 inch baking dish. Sprinkle the panko breadcrumbs evenly over the top. Bake for 20-25 minutes, or until the topping is golden brown and bubbly. It should smell absolutely divine, like pure comfort. Let it rest for a few minutes before serving, honestly, it's hard to wait, but it helps it set!

Notes

  1. Always roast your spaghetti squash until it's really tender, undercooked squash is tough and hard to shred.
  2. Whisk your milk into the roux gradually to avoid lumps in your cheese sauce, a lesson I learned the hard way.
  3. Freshly grate your cheese for the best melting and flavor – it's a small step that makes a huge difference!
  4. Serve with a crisp green salad to balance the richness of the au gratin.

Tools You'll Need

  • Baking sheet
  • large bowl
  • large saucepan or Dutch oven
  • 9x13 inch baking dish

Allergy Information

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

Nutrition Facts (Per Serving)

It is important to consider this information as approximate and not to use it as definitive health advice.
  • Calories: 350 kcal
  • Total Fat: 20g
  • Total Carbohydrate: 28g
  • Protein: 18g

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