Looking for a comforting yet guilt-free twist on a classic? This Healthy Spaghetti Squash Au Gratin is everything you want in a cozy side—cheesy, creamy, and perfectly golden on top without the heaviness of traditional versions. Using fresh spaghetti squash as a low-carb base and swapping in Greek yogurt for cream, this recipe balances nutrition and flavor effortlessly. Whether you’re cutting carbs or just craving something wholesome and satisfying, this dish delivers. Plus, it’s a fantastic make-ahead option for busy weeknights or meal-prepped lunches. Let’s dive into why this healthy gratin deserves a permanent spot on your table.
Healthy Spaghetti Squash Au Gratin: A Light, Cheesy Classic You’ll Love
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A cozy kitchen memory with a healthy twist
When I first made spaghetti squash au gratin, it was a cool October evening—the kind where you just want something warm and bubbling out of the oven. My mom used to make classic potato gratin with layers of heavy cream and butter, but I wanted something lighter without losing that creamy, cheesy goodness. That’s how Healthy Spaghetti Squash Au Gratin became a family favorite in my home.
Swapping in spaghetti squash gave me the perfect tender strands with a subtle sweetness. I used Greek yogurt instead of cream, and sharp cheddar gave it bold flavor with less cheese overall. The result? Comfort food without compromise.
This dish has become a go-to in our house—especially when I find a gorgeous squash at the farmers’ market. I love pairing it with a protein like this low-carb chicken casserole or keeping it simple with a salad and roasted veggies. And if you’re already a fan of lighter casseroles like our baked zucchini spinach and feta casserole, this one’s going to be a hit.
Why spaghetti squash works for gratin
Spaghetti squash is naturally low in calories and carbs, making it a smart substitute for pasta or potatoes in classic dishes. Once roasted, the flesh pulls apart into strands that mimic noodles—perfect for absorbing cheese and seasoning.
With its mild flavor, spaghetti squash allows the garlic, onion, and sharp cheddar to shine. It holds its shape without becoming mushy, especially when prepared right. If you’ve never tried it before, this dish is the perfect introduction.
Healthy ingredient swaps that keep it creamy, not heavy
Traditional au gratin recipes lean heavily on butter, flour, and heavy cream—but with a few simple swaps, you can enjoy that same creamy texture without all the saturated fat.
In this Healthy Spaghetti Squash Au Gratin, we use plain Greek yogurt instead of heavy cream or béchamel sauce. Greek yogurt brings creaminess, tang, and added protein without excess calories. Just a half cup is enough to bind the squash and create that rich, satisfying mouthfeel.
Sharp cheddar is another smart choice—it delivers maximum flavor, so you can use less cheese overall. A little paprika or thyme adds warmth and depth, and a touch of olive oil helps sauté the onion and garlic without needing butter.
Pair this lightened-up version with something equally wholesome, like our simple zucchini dill casserole or these stuffed zucchini boats for a balanced veggie-based spread.
| Traditional Ingredient | Healthy Swap |
|---|---|
| Heavy cream | Plain Greek yogurt |
| Butter | Olive oil |
| White potatoes | Spaghetti squash |
| All-purpose flour | No thickeners needed |
How to keep spaghetti squash from getting watery
One of the most common challenges with spaghetti squash recipes is excess moisture. Because the squash holds water, it’s important to prep it correctly to avoid a soggy gratin.
Here’s what works:
- Roast, don’t steam or microwave. Roasting at 400°F allows moisture to evaporate and gives the squash a richer texture.
- Salt and drain. After roasting and shredding the squash into strands, place them in a clean dish towel or paper towels. Squeeze out as much liquid as possible.
- Avoid overmixing. Once your squash is combined with yogurt and cheese, gently fold it—overmixing can release extra moisture.
Using these tips keeps your gratin firm and golden, not watery. If you’re looking for more baked veggie inspiration, check out this easy baked zucchini or our crispy and easy zucchini fritters, which follow similar techniques.
Flavor upgrades for next-level gratin
The beauty of a dish like Healthy Spaghetti Squash Au Gratin is how easily you can add layers of flavor with just a few pantry staples. Since the base is mild, it’s a perfect canvas for experimenting.
Start with a solid aromatic base—sautéed onion and garlic in olive oil give that essential depth. From there, adding paprika or dried thyme enhances warmth. You can even sprinkle a little smoked paprika on top before baking for a subtle kick.
Want to take it up a notch? Try stirring in a tablespoon of Parmesan for salty richness or adding a touch of Dijon mustard for brightness. These small tweaks make a big difference without adding extra calories.
For those who love veggie-packed casseroles, this dish pairs well with bold, cheesy dinners like our cheesy low-carb Philly cheesesteak casserole or a lighter lunch like zucchini noodle chicken alfredo.
How to bake it for a perfect golden top
Baking is where the magic happens—when the cheese melts, the edges bubble, and the top turns golden brown.
Preheat your oven to 375–400°F, depending on your oven’s strength. Use a lightly greased baking dish to keep the gratin from sticking. Spread the squash mixture evenly, then top with the remaining cheddar cheese. Don’t cover it—uncovered baking is what gives it that golden gratin crust.
Bake for 20–25 minutes, or until bubbly and the top is lightly browned. If you want an extra crispy top, broil it for the last 1–2 minutes, watching closely so it doesn’t burn.
You can also divide the mixture into smaller ramekins for individual servings—perfect for meal prep or portion control.
Serve it alongside a main like our steak and shrimp stir fry or with a crisp salad like peanut chili crisp cucumber salad for a light, complete meal.
How to store and reheat spaghetti squash gratin
One of the best things about Healthy Spaghetti Squash Au Gratin is how well it stores. Whether you’re meal prepping for the week or saving leftovers from dinner, this dish keeps its flavor and texture with the right storage.
To refrigerate: Let the gratin cool completely, then cover tightly or transfer to an airtight container. It will stay fresh in the fridge for up to 4 days.
To freeze: For longer storage, portion into freezer-safe containers or wrap individual servings in foil. Freeze for up to 2 months. Thaw overnight in the fridge before reheating.
To reheat: Place the gratin in an oven-safe dish, cover with foil, and bake at 350°F until heated through (about 15 minutes). For a crisp top, remove the foil during the last few minutes. You can also reheat individual portions in the microwave, but the oven gives the best texture.
This recipe also travels well for lunches. Just pack a square with a fresh salad, and you’ve got a nourishing midday meal that feels indulgent without the food coma.
Pair it with other prep-friendly dishes like chicken potato broccoli casserole or our high-protein cottage cheese flatbread for variety all week long.
Creative ways to serve leftovers
Leftover Healthy Spaghetti Squash Au Gratin can be more than just a side—get creative and turn it into something new!
Try spooning it into a wrap or pita with grilled chicken and a drizzle of hot sauce. Or use it as a bed for poached eggs in the morning, similar to a veggie-packed hash. You can even layer it into a roasted veggie lasagna or stuff it back into squash shells for a fun presentation.
It’s also a great meatless main when paired with something hearty like our philly cheesesteak bowls or as a base for a runny fried egg and avocado.
Print
Healthy Spaghetti Squash Au Gratin: A Light, Cheesy Classic You’ll Love
- Total Time: 55 minutes
- Yield: 4 servings 1x
Description
A lightened-up cheesy casserole with roasted spaghetti squash, Greek yogurt, and sharp cheddar. Creamy, satisfying, and low-carb!
Ingredients
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 thyme for extra flavor
Instructions
1. Preheat oven to 400°F. Slice spaghetti squash in half, scoop seeds, and roast cut-side down for 35–40 minutes.
2. Once cool, use a fork to scrape the strands. Place in a clean towel and squeeze out excess water.
3. In a pan, heat olive oil and sauté onion for 3–4 minutes. Add garlic and cook 1 minute more.
4. In a large bowl, mix Greek yogurt, half the cheese, sautéed onions, garlic, salt, pepper, and optional spices.
5. Fold in the squash strands gently.
6. Transfer to a greased baking dish. Top with remaining cheese.
7. Bake at 375°F for 20–25 minutes until bubbly and golden. Broil last 2 minutes if desired.
8. Cool slightly and serve warm.
Notes
Roast the squash to prevent sogginess. Don’t skip squeezing out water.
Store in fridge up to 4 days. Reheat covered in oven for best results.
- Prep Time: 15 minutes
- Cook Time: 40 minutes
- Category: Sides
- Method: Baked
- Cuisine: American
Nutrition
- Serving Size: 1 cup
- Calories: 210
- Sugar: 4g
- Sodium: 310mg
- Fat: 12g
- Saturated Fat: 6g
- Unsaturated Fat: 5g
- Trans Fat: 0g
- Carbohydrates: 12g
- Fiber: 2g
- Protein: 14g
- Cholesterol: 30mg
FAQ
Is spaghetti squash a healthy substitute for pasta?
Yes! Spaghetti squash is low in calories and carbs and offers fiber and vitamins. It’s a great substitute for pasta, especially in low-carb or gluten-free diets.
Can you make au gratin without heavy cream?
Absolutely. This recipe uses Greek yogurt instead of cream to keep it light while maintaining a creamy texture. You won’t miss the richness!
What cheese is best for a healthy au gratin?
Sharp cheddar is a smart choice because it delivers bold flavor in small amounts. You can also use part-skim mozzarella or a touch of Parmesan.
How do you keep spaghetti squash from getting watery?
Roast the squash instead of steaming it, and squeeze out excess moisture using paper towels. Avoid overmixing the strands once they’re prepped.
Conclusion
Healthy Spaghetti Squash Au Gratin is proof that comfort food can still be nourishing. With smart swaps and the right prep, you get a golden, cheesy bake that’s every bit as satisfying as the classic. It’s the kind of recipe that feels indulgent but fits seamlessly into a wholesome lifestyle. Whether you’re eating low-carb or just want a veggie-forward side, this dish is versatile, delicious, and sure to become a repeat on your table.
