Spaghetti Squash Au Gratin – Easy Creamy Casserole

Spaghetti squash au gratin is the perfect blend of comfort and nourishment — and from the very first forkful, you’ll be hooked. Imagine sweet strands of roasted squash soaked in a velvety cheese sauce, layered with nutty Gruyere, sharp cheddar, and a bubbly golden top that crackles when you break into it. The aroma? Buttery, garlicky, slightly nutty — enough to make your kitchen smell like a cozy bistro on a crisp fall day.

Whether you’re looking for an easy spaghetti squash au gratin recipe to impress guests, a healthy low-carb side dish, or just craving something creamy and soul-warming, this dish delivers. It’s one of those meals that feels indulgent yet secretly nutritious, making it perfect for family dinners, holidays, or make-ahead lunches.

This is the dish I make every year the moment squash season rolls in — it’s nostalgic, budget-friendly, and absolutely crowd-pleasing. Let’s dive in and get baking!

👉 Save this recipe, share it with your fellow squash lovers, and get ready to fall in love with this creamy, cheesy classic!

What Makes This So Irresistible

✅ Naturally low-carb and gluten-free-friendly
✅ Rich and creamy cheese sauce made from scratch
✅ Golden, crispy topping from baked cheese and panko
✅ Make-ahead friendly — perfect for holidays or busy weeks
✅ Customizable — add bacon, mushrooms, or greens
✅ Healthy comfort food without sacrificing flavor
✅ Simple ingredients and beginner-friendly instructions

Ingredients for Spaghetti Squash Au Gratin

🔸 For the Spaghetti Squash Base:

• 1 large spaghetti squash (about 3–4 pounds)
• 2 tablespoons unsalted butter, melted (for roasting)
• Salt and pepper to taste

🔸 For the Cheese Sauce:

• 2 tablespoons unsalted butter
• 1 medium yellow onion, finely chopped
• 2 cloves garlic, minced
• 4 tablespoons all-purpose flour
  (sub almond flour for gluten-free option)
• 3 cups whole milk (or unsweetened plant milk for dairy-free)
• ½ teaspoon salt, plus more to taste
• ¼ teaspoon black pepper
• ¼ teaspoon nutmeg

🔸 Cheese Mix:

• 1 cup grated Gruyere cheese, divided
• 1 cup grated sharp cheddar cheese, divided
• ½ cup grated Parmesan cheese, divided

🔸 Topping:

• ¼ cup panko breadcrumbs (or crushed pork rinds for keto)
• 2 tablespoons chopped fresh parsley for garnish (optional)

Optional: Homemade Cheese Sauce (From Scratch)

Already included in the instructions below, but this sauce is a classic base you can use for mac and cheese or veggie casseroles too!

How to Make Spaghetti Squash Au Gratin – Step by Step

🔹 Step 1: Preheat & Prep the Squash

Preheat your oven to 400°F (200°C). Carefully slice the squash in half lengthwise. If it’s too firm, microwave for 2–3 minutes to soften.

🔹 Step 2: Roast the Squash

Scoop out seeds and stringy center. Brush with melted butter, season with salt & pepper, and place cut-side down on a parchment-lined baking sheet.
Roast for 45–60 minutes until fork-tender.

🔹 Step 3: Shred the Squash

Let cool slightly, then use a fork to pull squash into spaghetti-like strands. Set aside.

🔹 Step 4: Make the Cheese Sauce

In a saucepan, melt 2 tbsp butter over medium heat. Add chopped onion and cook until translucent (5–7 minutes). Add garlic, cook 1 more minute.

🔹 Step 5: Make a Roux

Sprinkle in the flour, stirring constantly for 2 minutes. Slowly whisk in milk, a little at a time, until smooth.

🔹 Step 6: Simmer the Sauce

Bring to a gentle simmer, stirring, for 5–7 minutes or until slightly thickened. Add salt, pepper, and nutmeg.

🔹 Step 7: Add Cheese

Remove from heat. Stir in:

• ¾ cup Gruyere
• ¾ cup cheddar
• ¼ cup Parmesan
  Stir until melted and smooth.

🔹 Step 8: Combine Squash and Sauce

Fold the shredded squash into the cheese sauce until evenly coated.

🔹 Step 9: Assemble & Top

Transfer the mixture to a greased 9×13-inch baking dish. Mix remaining cheeses and breadcrumbs, then sprinkle over the top.

🔹 Step 10: Bake to Golden

Bake at 400°F for 20–25 minutes until the top is golden and bubbling.

🔹 Step 11: Rest & Serve

Let cool for 5–10 minutes to set. Garnish with parsley and serve hot!

Pro Tips & Cooking Secrets

💡 Use quality cheese – Gruyere and sharp cheddar give the deepest flavor.
💡 Don’t over-roast the squash – You want tender, not mushy strands.
💡 Double the batch – This reheats beautifully for leftovers!
💡 Spice it up – Add a pinch of red pepper flakes to the cheese sauce.
💡 Roast the squash earlier – It saves time on busy weeknights.
💡 Make it gluten-free – Swap flour for gluten-free blend and use GF panko.
💡 Add protein – Stir in cooked bacon, ham, or shredded chicken.
💡 Sneak in veggies – Add spinach or mushrooms for nutrition.
💡 Broil the top – For extra crispness, broil for 2–3 mins at the end.
💡 Use leftover squash – Great way to repurpose leftovers into a main dish.

Variations & Substitutions

🌶 Spicy Au Gratin – Add cayenne or hot sauce to the cheese mix.
🧀 Cheese Lover’s Edition – Add mozzarella or Fontina for extra melt.
🥬 Spinach Version – Stir in sautéed spinach before baking.
🍄 Mushroom Mix-In – Add caramelized mushrooms for umami depth.
🥦 Broccoli Boost – Toss in chopped, steamed broccoli.
🥦 Cauliflower Half & Half – Use 50/50 squash and roasted cauliflower.

Best Ways to Serve Spaghetti Squash Au Gratin

🍽 As a side dish – Pairs perfectly with roasted chicken or baked salmon.
🎉 Holiday table – A unique twist on gratins for Thanksgiving or Christmas.
🌱 Vegetarian entrée – Hearty enough to be the main meal.
🥗 With a fresh green salad – For a balanced, lighter dinner.
🧊 Meal prep – Portion and store for grab-and-go lunches.

Nutritional Information (Per Serving – Approximate)

• Calories: 390
• Fat: 25g
• Saturated Fat: 15g
• Protein: 18g
• Carbs: 22g
• Fiber: 6g
• Sugar: 8g
• Cholesterol: 90mg
• Sodium: 600mg

Storage & Reheating Guide

🧊 Refrigerator: Store leftovers in an airtight container for 3–4 days.
❄️ Freezer: Freeze fully baked gratin for up to 2 months.
🔥 Reheat in oven: 350°F for 15–20 mins until hot.
⚡ Microwave: 1–2 minutes per portion (texture may soften).
Tip: Sprinkle a bit of fresh cheese before reheating for best results.

Got Questions? We’ve Got You Covered

1. Can you make spaghetti squash au gratin ahead of time?

Yes, you can fully assemble spaghetti squash au gratin up to 24 hours in advance. Store it covered in the refrigerator, and bake just before serving. Add 5–10 minutes to the bake time if cooking from cold.

2. Is spaghetti squash au gratin low carb?

Yes, it’s naturally low in carbs, especially when made with gluten-free flour and without breadcrumbs. It’s a great alternative to traditional potato or pasta gratins.

3. What cheese works best for spaghetti squash au gratin?

Gruyere, sharp cheddar, and Parmesan are ideal. They melt beautifully and add nutty, bold flavors. Mozzarella, Fontina, or provolone can be added for variation.

4. How long does spaghetti squash au gratin last in the fridge?

Spaghetti squash au gratin will keep in the refrigerator for 3–4 days when stored in an airtight container. Reheat in the oven or microwave before serving.

5. Can I freeze spaghetti squash au gratin?

Yes! Freeze the fully baked (and cooled) gratin for up to 2 months. Thaw overnight in the fridge and reheat in the oven at 350°F until hot and bubbly.

More Tasty Ideas to Explore

• 30-Min Irresistible Brown Sugar Roasted Butternut Squash
• Cowboy Butter Chicken Linguine – Creamy Dinner Idea
• Garlic Bread Grilled Cheese | 15 min Lunch Idea

Savor the Ending

Now that you know how to make spaghetti squash au gratin, there’s no going back. Whether you’re eating lighter, going low-carb, or just looking for a creamy, cheesy, crave-worthy dish — this recipe checks all the boxes.

So go ahead, try it out, tweak it to your taste, and share your creation!

👇 Tell us: What’s your favorite twist on spaghetti squash au gratin?

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