There’s something deeply satisfying about a golden, bubbling gratin pulled straight from the oven, its cheesy aroma filling the entire kitchen. For years, I thought of it as a purely indulgent dish, reserved for special occasions. But then I discovered the magic of spaghetti squash. This incredible vegetable transforms into tender, noodle-like strands when cooked, providing the perfect base for a rich and creamy sauce without the heaviness of traditional potatoes or pasta. This Healthy Spaghetti Squash Au Gratin is the result of that discovery, a dish that delivers all the comforting character of a classic gratin in a much lighter, more wholesome package.

This is my go-to recipe when I need something that feels a bit special but is straightforward to put together on a weeknight. We’re swapping out heavy cream for a lighter, but still wonderfully luxurious, cheese sauce made with milk and a touch of crème fraîche. The nuttiness of the Gruyère cheese melts beautifully into the sweet, earthy flavour of the squash, all topped with a crisp, golden layer of Parmesan and breadcrumbs. It’s a fantastic low carb side dish that often steals the show, but it’s also substantial enough to enjoy as a main course with a simple green salad.

This recipe is for anyone looking to add more vegetables to their meals in a delicious way, or for those who adore a good squash casserole but want a healthier version. It works wonderfully for a family dinner – even my little ones are fans of the “cheesy spaghetti” – and it’s elegant enough to serve when you have friends over. It’s proof that eating well doesn’t mean sacrificing flavour or comfort.

Recipe Overview

This Healthy Spaghetti Squash Au Gratin is a beautifully balanced dish where tender strands of roasted squash are enveloped in a velvety, savoury cheese sauce and baked until golden and bubbly. The flavour is rich and nutty from the Gruyère, with a slight sweetness from the squash and a hint of warmth from nutmeg. When I was first testing this, I found that taking a moment to squeeze excess water from the cooked squash was the key to preventing a watery sauce and achieving that perfect creamy consistency.

• Prep Time: 20 minutes
• Cook Time: 45 minutes
• Total Time: 1 hour 5 minutes
• Servings: 6 as a side dish
• Difficulty: Easy

Why You’ll Love This Healthy Spaghetti Squash Au Gratin

• Genuine Flavour: The taste is genuinely complex and satisfying. You get the earthy sweetness of the roasted spaghetti squash, which pairs beautifully with the sharp, nutty notes of the Gruyère cheese. A pinch of nutmeg adds a subtle, warming spice that elevates the whole dish.
• Ready in Just Over an Hour: From start to finish, this impressive side dish comes together in about 65 minutes, with most of that time being hands-off while the squash and the final gratin are baking in the oven.
• Flexible Recipe: This recipe is very forgiving. You can easily swap the Gruyère for a strong, mature Cheddar or even a mix of cheeses. Feel free to stir in some cooked spinach or sautéed leeks for extra veg, or add some crispy bacon lardons for a smoky flavour.
• Great for Family Dinners: This is a brilliant way to get everyone to eat more vegetables. It works beautifully as a side dish for a Sunday roast, perhaps alongside our Grilled Lamb Chops, but it’s also hearty enough for a light meat-free main course.
• Family Tested: My family absolutely adores this creamy squash dish. The first time I made it, my husband was convinced it was a pasta bake. It always gets compliments and has become a firm favourite in our weekly meal rotation.

Healthy Spaghetti Squash Au Gratin

⏱️ 15 min prep  •  🍳 75 min cook  •  👥 4 servings

📌 Pin This Recipe

Ingredients You’ll Need

For this recipe, we’re using simple, wholesome ingredients to create that classic gratin experience. I always recommend using a good quality block of Gruyère cheese and grating it yourself; it melts so much more smoothly than pre-shredded varieties. My local supermarket does a fantastic cave-aged Gruyère that has an incredible depth of flavour.

• 1 medium spaghetti squash (about 1.2 kg)
• 1 tbsp olive oil
• Sea salt and freshly ground black pepper
• For the Sauce:
• 30g unsalted butter
• 30g plain flour
• 500ml semi-skimmed milk, warmed
• 100g Gruyère cheese, grated
• 50g Parmesan cheese, finely grated, divided
• 2 tbsp crème fraîche (or full-fat Greek yoghurt)
• 1 tsp Dijon mustard
• ¼ tsp grated nutmeg
• For the Topping:
• 30g panko breadcrumbs
• 1 tbsp fresh parsley, chopped

Ashley’s Tip: Don’t skip the nutmeg! It might seem like a small amount, but it’s a traditional component in a classic béchamel sauce and it makes a world of difference, adding a warmth that beautifully complements the cheese and squash.

How to Make Healthy Spaghetti Squash Au Gratin

The process for making this creamy squash casserole is quite straightforward. We’ll start by roasting the squash, then prepare a simple but flavourful cheese sauce to bring it all together before baking.

1. Prepare the Squash: Preheat your oven to 200°C (180°C fan). Carefully cut the spaghetti squash in half lengthways and scoop out the seeds. Drizzle the cut sides with olive oil and season generously with salt and pepper. Place cut-side down on a baking tray lined with parchment paper.
2. Roast the Squash: Roast for 30-40 minutes, or until the squash is tender and can be easily pierced with a fork. The exact time will depend on the size of your squash. Once cooked, remove from the oven and let it cool for about 10 minutes until it’s safe to handle.
3. Shred the Squash: Using a fork, scrape the flesh of the squash from the skin. It will naturally separate into long, noodle-like strands. Place the strands in a colander. I find that gently pressing the squash with the back of a spoon helps release any excess moisture, which is key for a creamy, not watery, final dish. You should have about 600-700g of cooked squash. Reduce the oven temperature to 190°C (170°C fan).
4. Start the Béchamel Sauce: While the squash cools, melt the butter in a medium saucepan over a medium heat. Whisk in the flour and cook for 1-2 minutes, stirring constantly, to form a paste (this is a roux).
5. Make the Cheese Sauce: Gradually pour in the warm milk, whisking continuously to prevent lumps. Continue to cook, stirring frequently, for 5-7 minutes until the sauce has thickened enough to coat the back of a spoon. Remove from the heat.
6. Finish the Sauce: Stir in the grated Gruyère, half of the Parmesan (25g), the crème fraîche, Dijon mustard, and grated nutmeg. Season with salt and pepper to taste. Keep stirring until the cheese is completely melted and the sauce is smooth and glossy.
7. Combine: Add the shredded spaghetti squash to the saucepan with the cheese sauce. Gently fold everything together until the squash strands are evenly coated in that glorious, creamy sauce.
8. Assemble the Gratin: Transfer the mixture to a 2-litre ovenproof baking dish and spread it out evenly.
9. Add the Topping: In a small bowl, mix the remaining 25g of Parmesan with the panko breadcrumbs and chopped parsley. Sprinkle this mixture evenly over the top of the squash.
10. Bake to Perfection: Bake for 20-25 minutes, until the topping is golden brown and the sauce is bubbling around the edges. Let it rest for 5 minutes before serving.

Tips From My Kitchen

• Temperature Control: When making the cheese sauce, be sure to add the cheese off the heat. If the sauce is boiling when you add the cheese, it can become oily or split. Taking it off the heat allows the cheese to melt gently into the sauce for a perfectly smooth texture.
• The Secret Step: I learned that giving the cooked spaghetti squash a gentle squeeze in a clean tea towel or a colander is the most important step for success. Spaghetti squash holds a lot of water, and removing it ensures your gratin is rich and creamy, never watery.
• Make-Ahead: You can assemble the entire gratin a day in advance. Simply prepare it up to step 9, cover tightly, and refrigerate. When you’re ready to bake, you may need to add an extra 5-10 minutes to the cooking time as it will be starting from cold.
• Storage: Leftovers can be stored in an airtight container in the refrigerator for up to 3 days. Reheat in the oven at 180°C (160°C fan) for 15-20 minutes or until heated through. I find the oven preserves the crispy topping much better than a microwave.

Delicious Variations to Try

One of the best things about this healthy gratin is how easily you can adapt it. Here are a few variations we love at home:

• Spicy Version: Add a generous pinch of red chilli flakes or a ¼ teaspoon of cayenne pepper to the cheese sauce along with the nutmeg for a gentle, warming heat that contrasts nicely with the creamy sauce.
• Vegetarian/Vegan Option: For a fully plant-based version, use a vegan butter and oat milk for the sauce. A good quality vegan Gruyère-style cheese and nutritional yeast will provide that cheesy flavour. Omit the crème fraîche or use a plant-based alternative.
• Different Protein: To make this a more substantial main meal, stir in about 200g of cooked, shredded chicken, crumbled cooked sausage, or crispy smoked bacon bits when you combine the squash and the sauce. It’s a great way to use up leftover roast chicken. For another great use of leftovers, try my recipe for Salmon Cakes.

What to Serve With Healthy Spaghetti Squash Au Gratin

This creamy squash casserole is versatile enough to be a star on its own or a fantastic supporting act. Here are a few of my favourite pairings:

• Roast Chicken or Fish: The gratin’s rich, cheesy flavour is a perfect match for the simplicity of a perfectly roasted chicken or a simple pan-fried fillet of salmon or cod.

– A Crisp Green Salad: A simple salad with a sharp, lemony vinaigrette cuts through the richness of the gratin beautifully, providing a fresh and light contrast.
– A Glass of White Wine: A crisp, dry white wine like a Sauvignon Blanc or an unoaked Chardonnay works wonderfully. The acidity complements the creamy sauce without overpowering the delicate squash flavour.

Frequently Asked Questions

Healthy Spaghetti Squash Au Gratin

A comforting, low-carb take on a classic gratin, featuring tender spaghetti squash strands enveloped in a creamy Gruyère and Parmesan cheese sauce, finished with a crispy panko topping.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 1 hour hr 15 minutes mins

Total Time 1 hour hr 30 minutes mins

Servings: 4 servings

Course: Main Course

Cuisine: American

Calories: 450

Ingredients Method Notes

Ingredients

  

• 1 medium spaghetti squash about 1.2 kg
• 1 tbsp olive oil
• Sea salt and freshly ground black pepper

For the Sauce

• 30 g unsalted butter
• 30 g plain flour
• 500 ml semi-skimmed milk warmed
• 100 g Gruyère cheese grated
• 50 g Parmesan cheese finely grated, divided
• 2 tbsp crème fraîche or full-fat Greek yoghurt
• 1 tsp Dijon mustard
• ¼ tsp grated nutmeg

For the Topping

• 30 g panko breadcrumbs
• 1 tbsp fresh parsley chopped

Method

 

1. Prepare the Squash: Preheat your oven to 200°C (180°C fan). Carefully cut the spaghetti squash in half lengthways and scoop out the seeds. Drizzle the cut sides with olive oil and season generously with salt and pepper. Place cut-side down on a baking tray lined with parchment paper.
2. Roast the Squash: Roast for 30-40 minutes, or until the squash is tender and can be easily pierced with a fork. The exact time will depend on the size of your squash. Once cooked, remove from the oven and let it cool for about 10 minutes until it's safe to handle.
3. Shred the Squash: Using a fork, scrape the flesh of the squash from the skin. It will naturally separate into long, noodle-like strands. Place the strands in a colander. I find that gently pressing the squash with the back of a spoon helps release any excess moisture, which is key for a creamy, not watery, final dish. You should have about 600-700g of cooked squash. Reduce the oven temperature to 190°C (170°C fan).
4. Start the Béchamel Sauce: While the squash cools, melt the butter in a medium saucepan over a medium heat. Whisk in the flour and cook for 1-2 minutes, stirring constantly, to form a paste (this is a roux).
5. Make the Cheese Sauce: Gradually pour in the warm milk, whisking continuously to prevent lumps. Continue to cook, stirring frequently, for 5-7 minutes until the sauce has thickened enough to coat the back of a spoon. Remove from the heat.
6. Finish the Sauce: Stir in the grated Gruyère, half of the Parmesan (25g), the crème fraîche, Dijon mustard, and grated nutmeg. Season with salt and pepper to taste. Keep stirring until the cheese is completely melted and the sauce is smooth and glossy.
7. Combine: Add the shredded spaghetti squash to the saucepan with the cheese sauce. Gently fold everything together until the squash strands are evenly coated in that glorious, creamy sauce.
8. Assemble the Gratin: Transfer the mixture to a 2-litre ovenproof baking dish and spread it out evenly.
9. Add the Topping: In a small bowl, mix the remaining 25g of Parmesan with the panko breadcrumbs and chopped parsley. Sprinkle this mixture evenly over the top of the squash.
10. Bake to Perfection: Bake for 20-25 minutes, until the topping is golden brown and the sauce is bubbling around the edges. Let it rest for 5 minutes before serving.

Notes

For extra flavor, add a clove of minced garlic to the butter before adding the flour. The dish can be assembled up to a day ahead, refrigerated, and then baked before serving.

I really hope this Healthy Spaghetti Squash Au Gratin becomes a new favourite in your home. It’s a wonderfully comforting and flavourful dish that proves healthy eating can be incredibly satisfying. It’s the kind of meal that makes a regular Tuesday feel a little more special. If you give it a try, I’d love to hear how it turned out for you. Please leave a comment below and let me know! Happy cooking, Ashley.