Looking for a comforting dish that won’t weigh you down? Healthy Spaghetti Squash Au Gratin is exactly what your dinner table needs. It’s cheesy, creamy, and cozy—without the carb overload of traditional casseroles. This recipe swaps out heavy ingredients for lighter, wholesome alternatives, but still delivers that bubbling, golden goodness we all crave. Whether you’re serving it at a holiday dinner or prepping for weekday lunches, this dish hits the sweet spot between indulgence and nutrition.

Why You’ll Love This Recipe

Spaghetti squash is a little miracle, isn’t it? It gives you those satisfying, noodle-like strands without the carbs, and it’s endlessly versatile. In this au gratin version, we roast the squash and mix it with savory aromatics, Greek yogurt, and sharp cheddar for a creamy, rich texture. Then we top it with Parmesan and bake until golden and bubbly. It’s the kind of dish you make once—and then crave every week after.

This recipe is:

Low-carb and gluten-free
Family-friendly (even the picky eaters will dive in)
Perfect for meal prep or special occasions
Easy to adapt with your favorite mix-ins

Ingredients Breakdown and Substitutions

Let’s take a closer look at what goes into this comforting bake—and how you can make it your own.

Spaghetti Squash: One medium squash is enough. Once roasted, it yields soft, fork-tender strands that soak up all that cheesy flavor.
Olive Oil: Just a touch to sauté your aromatics. Avocado oil works too.
Onion and Garlic: These are your base flavors—don’t skip them. They give this dish that cozy, savory depth.
Plain Greek Yogurt: Adds creaminess without the heaviness of sour cream or heavy cream. If you're more traditional, full-fat sour cream is a fine substitute.
Cheddar Cheese: Sharp cheddar gives the dish a bold, tangy kick. Feel free to mix in mozzarella for a stretchier, milder melt.
Parmesan Cheese: For that golden, salty crust on top.
Salt and Black Pepper: Season generously—squash loves salt.
Optional Herbs: Fresh thyme or chopped parsley takes this from good to unforgettable.

Want to add protein? Stir in cooked chicken or turkey before baking. You’ll have a full meal in one dish, perfect for leftovers too.

How to Prep Spaghetti Squash Like a Pro

Spaghetti squash can be a little intimidating to cut, especially if it’s your first time. But here’s the trick:
Microwave it whole for 2–3 minutes. This softens the skin just enough to make slicing it in half a breeze.

After that:

Slice the squash lengthwise.
Scoop out the seeds (just like you would with a pumpkin).
Place cut-side down on a parchment-lined baking sheet.
Roast at 400°F (200°C) for about 30–40 minutes.

You’ll know it’s ready when the squash strands easily pull apart with a fork. Let it cool slightly, then run a fork through the flesh to “shred” it into strands.

Tip: If your squash turns out watery, don’t panic. Just let the strands sit in a colander for 5–10 minutes to drain excess moisture before mixing.

Cooking Aromatics – Layering the Flavor

A good casserole starts with a flavor foundation, and that’s exactly what we’re building here.

Heat your olive oil in a skillet over medium heat. Add the chopped onion and cook until it’s soft and translucent—this takes about 4–5 minutes. Then stir in the minced garlic and cook for another minute. That’s it.

This step might seem small, but it adds a savory base that elevates the entire dish. You’re not just eating squash with cheese—you’re creating something comforting, rich, and deeply flavorful.

Optional Add-In: A pinch of red pepper flakes gives this just the right amount of heat if you’re into that.

Bringing It All Together – The Mixture

Now for the fun part: combining all the magic in one bowl.

In a large mixing bowl, add your cooked spaghetti squash strands. Toss in the sautéed onion and garlic, the Greek yogurt, most of your cheddar cheese (save a little for the topping), and season with salt and pepper.

Mix everything gently but thoroughly—you want the cheese and yogurt to coat the squash evenly.

Make it your own: This is a great spot to fold in extras like diced chicken, sautéed spinach, or chopped herbs. If you’re prepping meals ahead, divide the mixture into single-serve ramekins for easy reheating later.

Bake It to Golden Perfection

Now that your cheesy squash mixture is ready, it’s time to bake it into bubbly, golden perfection. Lightly grease a baking dish—an 8x8 works well—and spoon in the mixture, smoothing the top just a bit. Sprinkle the remaining cheddar over the surface, then finish it with a generous handful of grated Parmesan. This is where the magic happens.

Pop it in a 375°F oven and bake for 15 to 20 minutes. You're looking for a hot, bubbly center and a beautifully melted top. If you want that irresistibly crispy crust (and who doesn’t?), broil it for the last 2 minutes—just keep a close eye so it doesn’t burn.

Tip: Let it rest for 5–10 minutes before serving. This helps everything set up, and the flavors really come together as it cools just slightly.

Serving Suggestions and Add-ins

This dish is delicious on its own, but it also pairs beautifully with all kinds of proteins. Roasted chicken, pan-seared fish, or even Thanksgiving turkey fit right in. It’s cozy enough to serve on a holiday table and easy enough to whip up for a Tuesday night dinner.

If you’re into meal prepping, try dividing the gratin into individual ramekins before baking. It reheats like a dream, and you'll have single-serving portions ready to go. Just top with a fresh sprinkle of Parmesan before popping it back in the oven or microwave.

Want to bulk it up? Fold in some cooked shredded chicken, ground turkey, or even white beans before baking. The result is a filling, protein-packed main dish that still feels light and fresh.

Storage and Reheating Tips

Got leftovers? Lucky you. This gratin keeps well and tastes just as delicious the next day.

Refrigerator: Store in an airtight container for up to 4 days.
Freezer: Wrap tightly and freeze for up to 2 months. Thaw overnight in the fridge before reheating.
Reheat: Cover and warm in a 350°F oven until heated through. If using the microwave, add a splash of milk or broth to help revive the creamy texture.

Tip: If you’re reheating from frozen, bake it straight from the freezer at 350°F—just plan for 30–35 minutes.

Variations to Try Next Time

The beauty of this dish is how easily it adapts to your cravings and what’s in your fridge. Once you’ve mastered the base, here are a few delicious ways to switch things up:

Spinach and Feta: Add sautéed spinach and crumbled feta for a Mediterranean twist.
Sun-dried Tomatoes and Basil: For a burst of flavor and color.
Smoky Bacon or Turkey Sausage: Stir into the mix before baking for a heartier feel.
Vegan Swap: Use dairy-free yogurt and cheese—there are plenty of great options out there now.

Don’t be afraid to get creative. Once you have the method down, the variations are endless.

Healthy Spaghetti Squash Au Gratin FAQs

Is spaghetti squash au gratin low carb?
Yes, it’s naturally low in carbs thanks to the squash base and the use of Greek yogurt instead of cream. It’s a smart swap for traditional potato or pasta-based gratins.

What does “au gratin” mean?
It refers to dishes that are baked with a browned crust—usually from cheese or breadcrumbs. In this case, Parmesan stands in for breadcrumbs and gives you that golden, crispy top.

How do I keep spaghetti squash from getting watery?
Let the cooked squash rest in a colander to release excess moisture. Also, avoid oversalting—it can draw water out of the squash.

Is this a casserole or a gratin?
Technically, it’s both. A gratin is a type of casserole topped with cheese or crumbs and baked. So you’re getting the best of both worlds.

What should I serve with it?
Roasted chicken, baked salmon, or even turkey meatballs all work well. You can also serve it alongside a fresh green salad for a lighter meal.

Related Recipes

If you enjoyed this healthy spaghetti squash au gratin, check out these wholesome and comforting dishes from Jennifer Recipes:

Spinach Artichoke Chicken Casserole: A cheesy bake filled with spinach, artichoke, and juicy chicken.
Chicken Broccoli Rice Casserole: A hearty one-dish meal loaded with flavor.
Creamy Shrimp Tomato Pasta: A comforting seafood pasta perfect for a weeknight dinner.
Minestrone Soup: A veggie-packed soup to pair with your au gratin.
Grilled Ratatouille: A flavorful, roasted vegetable medley to serve alongside.

Final Thoughts – Your Cozy, Cheesy, Healthy Favorite

There’s something deeply satisfying about a dish that checks all the boxes: creamy, flavorful, comforting—and secretly healthy. Spaghetti Squash Au Gratin brings all of that to the table and more. Whether you’re feeding your family, prepping lunches for the week, or just treating yourself to something warm and nourishing, this recipe delivers.

Healthy Spaghetti Squash Au Gratin

Save Recipe

This healthy spaghetti squash au gratin is a creamy, cheesy, low-carb comfort dish made with Greek yogurt, sharp cheddar, and roasted squash. It’s gluten-free, family-friendly, and perfect as a side or light main dish.

Total Time: 1 hour 5 minutes
Yield: 4 servings 1x

Ingredients

Scale

1 medium spaghetti squash
1 tbsp olive oil
1 small onion, finely chopped
2 cloves garlic, minced
½ cup plain Greek yogurt
1 cup shredded sharp cheddar cheese
¼ cup grated Parmesan cheese
Salt and black pepper, to taste
Optional: Fresh thyme or parsley for garnish

Instructions

Preheat oven to 400°F (200°C). Slice squash in half lengthwise and remove seeds.
Place squash cut-side down on a baking sheet and roast for 30–40 minutes until tender.
Let squash cool slightly, then scrape strands into a bowl.
Heat olive oil in a skillet, sauté onion until soft, add garlic, and cook 1 more minute.
Add sautéed onion/garlic, yogurt, ¾ cup cheddar, salt, and pepper to squash. Mix well.
Transfer mixture to a greased baking dish. Top with remaining cheddar and Parmesan.
Bake at 375°F (190°C) for 15–20 minutes until bubbly and golden. Broil last 2 mins for a crispy top.
Let rest for 5–10 minutes before serving. Garnish with fresh herbs.

Notes

Drain squash in a colander if too watery.
Sub sour cream for yogurt if preferred.
Add cooked chicken or turkey for a heartier version.
Divide into ramekins for meal prep.

Author: Jennifer
Prep Time: 15 minutes
Cook Time: 50 minutes
Category: Side Dish
Method: Baking
Cuisine: American
Diet: Gluten Free

Nutrition

Serving Size: ¼ of recipe
Calories: 210
Sugar: 4g
Sodium: 280mg
Fat: 13g
Saturated Fat: 6g
Unsaturated Fat: 6g
Trans Fat: 0g
Carbohydrates: 10g
Fiber: 2g
Protein: 12g
Cholesterol: 30mg

Keywords: spaghetti squash au gratin, low-carb casserole, healthy side dish, gluten-free comfort food