If you’re on the lookout for a comforting yet nutritious dish that won’t weigh you down, this Healthy Spaghetti Squash Au Gratin Recipe is about to become your new favorite. Imagine the tender, tender strands of roasted spaghetti squash wrapped in a creamy, flavorful blend of Greek yogurt, Parmesan, and melty mozzarella, all perfectly seasoned with herbs like thyme and oregano. It’s the classic cozy spirit of au gratin with a clean, health-conscious twist that will satisfy your cravings and nourish your body without an ounce of guilt.

Ingredients You’ll Need
Every ingredient in this recipe plays a crucial role in balancing flavor, texture, and nutrition, making it surprisingly simple yet wonderfully satisfying. From the naturally low-carb spaghetti squash to the creamy tang of Greek yogurt, each component enhances the dish’s wholesome appeal and indulgent feel.
- 1 medium-sized spaghetti squash: The star of the show, its strands provide a tender, pasta-like base that’s naturally gluten-free.
- 1 tablespoon olive oil: Adds a subtle fruitiness and helps sauté the aromatics to perfection.
- 1 small onion, finely chopped: Brings sweetness and depth to the sautéed base.
- 2 cloves garlic, minced: Offers a warm, fragrant punch that complements the dish beautifully.
- 1/2 cup low-fat Greek yogurt: A creamy substitute that adds protein and tang without heavy cream or butter.
- 1/2 cup grated Parmesan cheese: Delivers umami richness and helps bind the flavors together.
- 1/2 teaspoon dried thyme: An earthy herb that lifts the entire dish.
- 1/2 teaspoon dried oregano: Adds a classic savory note, tying everything into a Mediterranean vibe.
- Salt and pepper to taste: Essential for balancing and enhancing all the flavors.
- 1/2 cup shredded mozzarella cheese: Creates that irresistibly gooey, golden crust that makes au gratin so crave-worthy.
- Fresh parsley for garnish: Adds a fresh burst of color and brightness on top.
How to Make Healthy Spaghetti Squash Au Gratin Recipe
Step 1: Prepare and Roast the Spaghetti Squash
Start by preheating your oven to 400°F (200°C). Carefully slice the spaghetti squash lengthwise and scoop out the seeds. Placing the halves face down on a baking sheet allows the flesh to steam and tenderize evenly as it roasts for 35-40 minutes. When done, it should easily shred into flossy strands that resemble pasta—this is where the magic begins!
Step 2: Sauté Aromatics for a Flavor Base
While the squash roasts, warm up your olive oil in a skillet over medium heat. Add the finely chopped onion and minced garlic, sautéing until the onion turns translucent and fragrant. This simple step develops a sweet and savory foundation that really brings depth to the final dish.
Step 3: Mix the Creamy Yogurt Sauce
In a mixing bowl, combine the sautéed onion and garlic with the Greek yogurt, grated Parmesan, thyme, oregano, and a pinch of salt and pepper. Stir everything together gently. This silky mixture will coat the spaghetti squash strands, creating the signature creamy texture of this healthy take on au gratin.
Step 4: Combine Squash with Sauce
Once the squash has cooled slightly, use a fork to shred the flesh into strands right inside a large bowl. Pour your yogurt and cheese mixture over the strands, folding it in until the squash is evenly coated. This mixture is already irresistible but trust me, the best is yet to come.
Step 5: Bake to Golden Perfection
Transfer the squash and sauce mix into a baking dish. Sprinkle the shredded mozzarella cheese evenly across the top, covering every inch. Bake the dish at 400°F for about 20 minutes, or until the cheese melts into a bubbly, golden-brown crust. This final step transforms a simple casserole into a decadent and satisfying meal.
Step 6: Garnish and Serve Warm
Allow the au gratin to cool just enough to settle, then sprinkle fresh parsley over the top for a vibrant splash of color and fresh herbal brightness. Serve it warm, straight from the oven, and enjoy the irresistible combination of creamy, cheesy, and herbaceous flavors that make this Healthy Spaghetti Squash Au Gratin Recipe so special.
How to Serve Healthy Spaghetti Squash Au Gratin Recipe

Garnishes
Fresh parsley is the classic garnish here, adding a pop of green and a fresh finish that balances the richness. For a little extra zing, you could add a light dusting of smoked paprika or a sprinkle of toasted pine nuts for crunch. These garnishes make the dish even more visually inviting and texturally interesting.
Side Dishes
This au gratin shines as a delightful main dish but pairs beautifully with a bright green salad or some roasted seasonal vegetables. A simple arugula salad with lemon vinaigrette is a perfect contrast, cutting through the creaminess with its peppery bite. You could also serve this alongside grilled chicken or fish for a well-rounded meal.
Creative Ways to Present
For a festive dinner, serve this Healthy Spaghetti Squash Au Gratin Recipe in individual ramekins instead of one big dish. This creates a charming presentation that’s perfect for entertaining or a cozy date night at home. Layering the squash mixture and cheese in a clear baking dish also shows off the beautiful textures and colors when served family style.
Make Ahead and Storage
Storing Leftovers
Leftover au gratin stores beautifully in an airtight container in the refrigerator for up to 3 days. The flavors even deepen overnight, making for a comforting next-day meal. Just be sure to cool the dish completely before refrigerating to preserve texture and freshness.
Freezing
If you want to save this recipe for longer, freezing is an option. Transfer portions into freezer-safe containers or bags and freeze for up to 2 months. When you’re ready to enjoy it again, thaw overnight in the fridge for best results—this will prevent excess moisture and maintain the creamy texture.
Reheating
Reheat gently in the oven at 350°F until warmed through and the cheese is bubbly again, about 15-20 minutes. You can also reheat in the microwave, though the oven method keeps the top crispy and more enjoyable. Add a little sprinkle of fresh parsley after reheating to refresh the flavors.
FAQs
Can I use a different type of squash?
While spaghetti squash is ideal for its unique texture that mimics pasta, you could try butternut or acorn squash, though the final dish will be creamier and less stringy. The au gratin style still works wonderfully, just expect a slightly different mouthfeel.
Is this recipe dairy-free?
This version includes dairy cheeses and yogurt for that authentic au gratin creaminess. However, you could substitute vegan cheese and dairy-free yogurt alternatives to make it dairy-free—just keep in mind the flavor and texture will vary slightly.
How can I add more protein?
Adding cooked chicken, turkey, or even some cooked lentils into the squash mixture before baking is an excellent way to boost protein. The Greek yogurt already contributes protein, but these additions make the meal more filling.
Can I make this recipe vegan?
You can make a vegan version by swapping out the Parmesan and mozzarella for plant-based cheeses and using plant-based yogurt alternatives. Nutritional yeast can be added for a cheesy flavor boost. It’s a tasty variation that still honors the original flavors.
What can I substitute for Greek yogurt?
If you don’t have Greek yogurt, sour cream or a thick crème fraîche can work in a pinch, but Greek yogurt keeps the dish tangy and light. For non-dairy options, try a coconut-based yogurt or cashew cream for creaminess without lactose.
Final Thoughts
This Healthy Spaghetti Squash Au Gratin Recipe is one of those dishes that feels indulgent but is actually nourishing and wholesome, perfect for anyone wanting to enjoy comfort food with a healthy twist. It’s approachable, packed with flavor, and a fantastic way to rethink traditional au gratin for a lighter lifestyle. I can’t wait for you to make it and share it with your favorite people—once you try it, this recipe will be a delicious staple in your kitchen too!
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Healthy Spaghetti Squash Au Gratin Recipe
- Prep Time: 0h 15m
- Cook Time: 1h 0m
- Total Time: 1h 15m
- Yield: 4 servings
- Category: Side Dish
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
This Healthy Spaghetti Squash Au Gratin offers a nutritious and delicious alternative to traditional cheesy gratin dishes. Roasted spaghetti squash strands are combined with a savory mixture of sautéed onions, garlic, low-fat Greek yogurt, Parmesan, and herbs, then topped with melted mozzarella for a creamy, comforting meal that’s lower in calories and fat.
Ingredients
Main Ingredients
- 1 medium-sized spaghetti squash
- 1 tablespoon olive oil
- 1 small onion, finely chopped
- 2 cloves garlic, minced
- 1/2 cup low-fat Greek yogurt
- 1/2 cup grated Parmesan cheese
- 1/2 teaspoon dried thyme
- 1/2 teaspoon dried oregano
- Salt and pepper to taste
- 1/2 cup shredded mozzarella cheese
- Fresh parsley for garnish
Instructions
- Preheat Oven: Preheat your oven to 400°F (200°C) to prepare for roasting the squash.
- Prepare Squash: Cut the spaghetti squash in half lengthwise and carefully remove the seeds to make roasting easier.
- Roast Squash: Place the squash halves face down on a baking sheet and roast for 35-40 minutes until the flesh is tender and can be shredded with a fork.
- Sauté Aromatics: While the squash roasts, heat olive oil in a skillet over medium heat. Add onion and garlic and sauté until the onion is translucent and fragrant.
- Make Yogurt Mixture: In a mixing bowl, combine the cooked onion and garlic with Greek yogurt, Parmesan cheese, dried thyme, oregano, salt, and pepper. Stir well to integrate all flavors.
- Shred Squash Flesh: Once the squash is cool enough to handle, use a fork to scrape the flesh into spaghetti-like strands and transfer to a large bowl.
- Combine Mixture: Add the yogurt and cheese mixture to the shredded squash and stir until everything is evenly combined.
- Assemble Dish: Transfer the mixture into a baking dish and evenly sprinkle shredded mozzarella cheese over the top.
- Bake Au Gratin: Return the baking dish to the oven and bake for an additional 20 minutes until the cheese on top melts and turns golden brown.
- Garnish and Serve: Allow the dish to cool slightly, then garnish with fresh parsley before serving warm for a comforting side or main dish.
Notes
- Spaghetti squash size can vary; adjust cooking time if needed to ensure tenderness.
- Low-fat Greek yogurt keeps the dish creamy but lighter than traditional cream or heavy cheese bases.
- You can add more herbs like basil or rosemary for different flavor profiles.
- Use fresh mozzarella instead of shredded for a creamier topping if desired.
- This dish is suitable as a vegetarian main or side.

