Healthy Spaghetti Squash Au Gratin
If you’re looking for a dish that feels like a warm hug on a plate, then this Healthy Spaghetti Squash Au Gratin is just what you need. It’s creamy, cheesy, and packed with wholesome ingredients that make it perfect for any occasion—from busy weeknights to festive family gatherings. I love how this recipe combines the comfort of traditional au gratin with the benefits of fresh veggies. It’s truly a winner in my kitchen, and I’m excited to share it with you!
What makes this dish even more special is its versatility. You can serve it as a delightful side or enjoy it as a light main course. Plus, it’s naturally low-carb and gluten-free, making it suitable for many dietary preferences. Trust me; once you try it, you’ll want to keep this recipe in your back pocket!
Why You’ll Love This Recipe
- Easy to Prepare: With simple steps and minimal fuss, this dish comes together quickly, making it perfect for busy evenings.
- Family-Friendly: Even picky eaters will love the cheesy goodness packed into every bite.
- Make Ahead Convenience: You can prepare this ahead of time and pop it in the oven when you’re ready to enjoy.
- Delicious Flavor: The combination of roasted spaghetti squash, creamy yogurt, and sharp cheddar creates an unforgettable taste sensation.

Ingredients You’ll Need
This recipe calls for simple, wholesome ingredients that you likely already have in your kitchen. Here’s what you’ll need:
For the Main Dish
- 1 medium spaghetti squash
- 1 tbsp olive oil
- ½ cup diced onion
- 2 cloves garlic (minced)
- ½ cup plain Greek yogurt (or sour cream)
- 1½ cups shredded sharp cheddar cheese (divided)
- ¼ tsp salt
- ¼ tsp black pepper
- Optional: ¼ tsp paprika or dried thyme
Variations
One of the best things about this Healthy Spaghetti Squash Au Gratin is its flexibility. You can easily tweak ingredients based on what you have on hand or your personal preferences.
- Add More Veggies: Toss in some sautéed spinach or chopped bell peppers for extra nutrition and color.
- Change the Cheese: Swap out sharp cheddar for mozzarella or gouda if you prefer a milder flavor.
- Spice It Up: Add some crushed red pepper flakes for a little kick!
- Make It Vegan: Replace Greek yogurt with a plant-based alternative and use vegan cheese to keep it dairy-free.
How to Make Healthy Spaghetti Squash Au Gratin
Step 1: Roast the Spaghetti Squash
Preheat your oven to 400°F (205°C). Slice the spaghetti squash in half lengthwise and scoop out the seeds. Brushing the cut sides with olive oil helps them roast beautifully while enhancing their flavor. Place them face-down on a baking sheet and roast for 35–40 minutes until tender. This step is essential as roasting brings out that lovely sweetness in the squash.
Step 2: Sauté Onions and Garlic
While your squash roasts, heat a skillet over medium heat and add a little olive oil. Sauté the diced onions until they soften—about five minutes—and then add minced garlic for one more minute. This aromatic combo is going to add depth to our dish!
Step 3: Shred the Squash
Once your roasted spaghetti squash is cool enough to handle, grab a fork and shred it into noodle-like strands. This step transforms our main ingredient into delightful “spaghetti” that will soak up all those tasty flavors.
Step 4: Mix Everything Together
In a large bowl, combine your shredded squash with the sautéed onions and garlic, Greek yogurt (or sour cream), one cup of shredded cheese, salt, pepper, and optional spices like paprika or thyme. This mixture is where all those comforting flavors meld together beautifully!
Step 5: Bake It Up
Transfer your mixture into a greased casserole dish and sprinkle the remaining half cup of cheese on top. Bake at 375°F (190°C) for about 20–25 minutes until hot and bubbly with a gorgeous golden top! This final baking step ensures everything is heated through while giving us that satisfying cheesy crust.
Step 6: Serve and Enjoy
Let your Healthy Spaghetti Squash Au Gratin cool slightly before serving up this deliciousness! Whether as a side dish or light main course, I’m sure everyone will be coming back for seconds! Enjoy!
Pro Tips for Making Healthy Spaghetti Squash Au Gratin
Making this delightful dish even better is all about the little tweaks! Here are some pro tips to ensure your Healthy Spaghetti Squash Au Gratin turns out perfectly every time.
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Choose the right squash: Look for a spaghetti squash that feels heavy for its size and has a smooth, unblemished skin. This indicates freshness and quality, ensuring your dish has the best flavor and texture.
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Don’t skip the roasting: Roasting the spaghetti squash brings out its natural sweetness and enhances its flavor. It also helps reduce excess moisture, preventing your au gratin from becoming soggy.
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Experiment with cheeses: While sharp cheddar adds a wonderful flavor, feel free to mix in other cheeses like mozzarella or Gouda for a unique twist. Each cheese offers a different taste and creaminess that can elevate your dish.
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Add veggies: For an extra nutrient boost, consider folding in additional vegetables like spinach or bell peppers into the mixture. This not only enhances the nutritional profile but also adds vibrant colors to your dish.
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Let it rest: After baking, allow your au gratin to sit for about 5 minutes before serving. This resting period allows it to set up slightly, making it easier to serve and enjoy!
How to Serve Healthy Spaghetti Squash Au Gratin
This Healthy Spaghetti Squash Au Gratin is not just delicious but also visually appealing—perfect for impressing family and friends! Here are some ideas on how to present this comforting dish beautifully.
Garnishes
- Fresh herbs: Sprinkle chopped fresh parsley or chives on top just before serving for a pop of color and fresh flavor.
- Cracked pepper: A dash of freshly cracked black pepper adds a subtle spice that complements the richness of the cheese.
Side Dishes
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Simple Green Salad: A light salad with mixed greens, cherry tomatoes, and a lemon vinaigrette makes for a refreshing counterpart to the creamy gratin.
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Roasted Vegetables: Seasonal roasted vegetables such as carrots, zucchini, or Brussels sprouts provide a crunchy texture that balances out the softness of the au gratin.
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Garlic Bread: Crispy garlic bread is always a hit! Its crunchy exterior and buttery flavor pair well with the creamy nature of the dish.
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Quinoa Pilaf: A fluffy quinoa pilaf with nuts and dried fruit offers a nutritious contrast to the cheesy gratin while adding an element of heartiness.
Now you have everything you need to make this scrumptious Healthy Spaghetti Squash Au Gratin shine on your dinner table! Enjoy every bite!

Make Ahead and Storage
This Healthy Spaghetti Squash Au Gratin is perfect for meal prep, making it easy to enjoy throughout the week. You can prepare it ahead of time and store it for later, ensuring you always have a delicious, wholesome dish on hand.
Storing Leftovers
- Allow the dish to cool completely before storing.
- Transfer leftovers to an airtight container.
- Store in the refrigerator for up to 3–4 days.
Freezing
- Cool the dish completely before freezing.
- Portion out into freezer-safe containers or wrap tightly in plastic wrap.
- Freeze for up to 2 months.
Reheating
- Thaw overnight in the refrigerator if frozen.
- Reheat in the oven at 350°F (175°C) for about 15–20 minutes until heated through.
- Alternatively, reheat in the microwave in short bursts until warm.
FAQs
Here are some common questions you may have about this delicious recipe!
Can I make Healthy Spaghetti Squash Au Gratin without cheese?
Absolutely! You can substitute nutritional yeast for cheese to maintain a cheesy flavor while keeping it dairy-free.
How long does Healthy Spaghetti Squash Au Gratin last in the fridge?
This dish will last for about 3–4 days when stored properly in an airtight container in the refrigerator.
Can I use other vegetables in Healthy Spaghetti Squash Au Gratin?
Yes! Feel free to add veggies like spinach, bell peppers, or mushrooms to customize your gratin and boost its nutrition.
Is Healthy Spaghetti Squash Au Gratin suitable for gluten-free diets?
Yes! This recipe is naturally gluten-free as it uses spaghetti squash instead of traditional pasta or breadcrumbs.
Final Thoughts
I hope you enjoy making this Healthy Spaghetti Squash Au Gratin as much as I do! It’s a cozy, comforting dish that’s both nutritious and satisfying. Whether you’re serving it as a side or making it the star of your meal, it’s sure to please everyone at your table. Happy cooking, and don’t forget to share your thoughts on this recipe!
Healthy Spaghetti Squash Au Gratin
Enjoy a creamy and healthy twist on comfort food with our Healthy Spaghetti Squash Au Gratin. Try this easy recipe today!
- Prep Time: 15 minutes
- Cook Time: 45 minutes
- Total Time: 1 hour
- Yield: Serves approximately 6 people 1x
- Category: Main
- Method: Baking
- Cuisine: American
Ingredients
- 1 medium spaghetti squash
- 1 tbsp olive oil
- ½ cup diced onion
- 2 cloves garlic (minced)
- ½ cup plain Greek yogurt
- 1½ cups shredded sharp cheddar cheese (divided)
- ¼ tsp salt
- ¼ tsp black pepper
- Optional: ¼ tsp paprika or dried thyme
Instructions
- Preheat the oven to 400°F (205°C). Halve the spaghetti squash lengthwise, scoop out the seeds, brush with olive oil, place cut-side down on a baking sheet, and roast for 35–40 minutes until tender.
- In a skillet over medium heat, sauté diced onions in olive oil until softened (about 5 minutes), then add minced garlic for another minute.
- Once cool enough to handle, shred the roasted spaghetti squash into strands with a fork.
- In a large bowl, combine shredded squash with sautéed onions and garlic, Greek yogurt, 1 cup of cheese, salt, pepper, and optional spices.
- Transfer to a greased casserole dish, sprinkle remaining cheese on top, and bake at 375°F (190°C) for 20–25 minutes until bubbly.
Nutrition
- Serving Size: 1 cup (240g)
- Calories: 250
- Sugar: 3g
- Sodium: 320mg
- Fat: 15g
- Saturated Fat: 7g
- Unsaturated Fat: 8g
- Trans Fat: 0g
- Carbohydrates: 20g
- Fiber: 6g
- Protein: 10g
- Cholesterol: 30mg