This Healthy Spaghetti Squash Au Gratin is a delightful dish that brings comfort and nutrition to your table. Perfect for weeknight dinners or special occasions, this recipe combines the lightness of spaghetti squash with creamy Greek yogurt and sharp cheddar cheese. It’s naturally low-carb and gluten-free, making it a fantastic option for those looking to indulge without the guilt. You’ll love how simple it is to prepare, yet it delivers on flavor and satisfaction.

Jump to:
- Why You’ll Love This Recipe
- Tools and Preparation
- Essential Tools and Equipment
- Importance of Each Tool
- Ingredients
- For the Spaghetti Squash
- For the Filling
- For the Cheese Mixture
- How to Make Healthy Spaghetti Squash Au Gratin
- Step 1: Preheat the Oven
- Step 2: Prepare the Spaghetti Squash
- Step 3: Sauté Onions and Garlic
- Step 4: Shred the Squash
- Step 5: Combine Ingredients
- Step 6: Transfer to Casserole Dish
- Step 7: Bake
- Step 8: Serve
- How to Serve Healthy Spaghetti Squash Au Gratin
- As a Main Dish
- As a Side Dish
- For Meal Prep
- How to Perfect Healthy Spaghetti Squash Au Gratin
- Best Side Dishes for Healthy Spaghetti Squash Au Gratin
- Common Mistakes to Avoid
- Storage & Reheating Instructions
- Refrigerator Storage
- Freezing Healthy Spaghetti Squash Au Gratin
- Reheating Healthy Spaghetti Squash Au Gratin
- Frequently Asked Questions
- Can I make Healthy Spaghetti Squash Au Gratin ahead of time?
- What can I substitute for Greek yogurt?
- How do I know when the spaghetti squash is done cooking?
- Can I customize the Healthy Spaghetti Squash Au Gratin?
- Final Thoughts
- 📖 Recipe Card
Why You’ll Love This Recipe
- Rich Flavor: The combination of sautéed onions, garlic, and sharp cheddar creates a deliciously cheesy taste that pleases everyone.
- Versatile Dish: Enjoy it as a side or a light main course; this dish works well for any meal!
- Healthy Ingredients: With spaghetti squash as the base and Greek yogurt for creaminess, you get a nutritious meal without sacrificing taste.
- Easy Preparation: Simple steps ensure that even beginner cooks can make this delightful dish without hassle.
- Make Ahead Option: Prepare in advance and bake just before serving for a stress-free meal.

Tools and Preparation
Before you begin cooking, gather your tools. Having everything ready will make the cooking process smoother.
Essential Tools and Equipment
- Baking sheet
- Skillet
- Casserole dish
- Fork
- Mixing bowl
Importance of Each Tool
- Baking sheet: Essential for roasting the spaghetti squash evenly, ensuring perfect tenderness.
- Skillet: Used for sautéing onions and garlic, which enhances their flavors before adding them to the mix.
- Casserole dish: Ideal for baking the au gratin, allowing it to heat through completely while achieving a golden crust.
Ingredients
For the Spaghetti Squash
- 1 medium spaghetti squash
- 1 tbsp olive oil
For the Filling
- ½ cup diced onion
- 2 cloves garlic (minced)
- ½ cup plain Greek yogurt (or sour cream)
For the Cheese Mixture
- 1½ cups shredded sharp cheddar cheese (divided)
- ¼ tsp salt
- ¼ tsp black pepper
- Optional: ¼ tsp paprika or dried thyme
How to Make Healthy Spaghetti Squash Au Gratin
Step 1: Preheat the Oven
Preheat your oven to 400°F (205°C). This ensures that your spaghetti squash roasts perfectly.
Step 2: Prepare the Spaghetti Squash
- Slice the spaghetti squash in half lengthwise and scoop out seeds.
- Brush cut sides with olive oil.
- Place face-down on a baking sheet.
- Roast for 35–40 minutes or until tender.
Step 3: Sauté Onions and Garlic
- Heat a skillet over medium heat.
- Add onions and sauté in olive oil until softened (about 5 minutes).
- Add minced garlic and cook for an additional minute before removing from heat.
Step 4: Shred the Squash
Once cool enough to handle, use a fork to shred the roasted squash into noodle-like strands.
Step 5: Combine Ingredients
In a large bowl, mix shredded squash with sautéed onions and garlic, Greek yogurt, 1 cup of cheese, salt, pepper, and optional paprika or thyme.
Step 6: Transfer to Casserole Dish
Transfer mixture into a greased casserole dish. Top with remaining ½ cup of cheese.
Step 7: Bake
Bake at 375°F for 20–25 minutes until hot and bubbly with a golden top.
Step 8: Serve
Let cool slightly before serving. Enjoy this Healthy Spaghetti Squash Au Gratin as a side dish or light main!
How to Serve Healthy Spaghetti Squash Au Gratin
Healthy Spaghetti Squash Au Gratin is a versatile dish that can be enjoyed in various ways. Whether you’re planning a family dinner or a holiday gathering, here are some serving suggestions to make the most of this delicious meal.
As a Main Dish
- Pair with a fresh green salad for a light yet filling meal. The crunch of the salad complements the creamy gratin beautifully.
- Serve alongside grilled chicken or fish for added protein, making it a well-rounded dinner option.
As a Side Dish
- Accompany your favorite roasted meats with this gratin; it’s an excellent side that adds flavor and nutrition to any plate.
- Offer as part of a vegetarian spread, perfect for gatherings where guests may prefer plant-based options.
For Meal Prep
- Portion out leftovers into individual containers for quick lunches throughout the week. It reheats well and retains its flavor.
- Freeze portions for later use; simply thaw and bake until heated through when you’re ready to enjoy again.
How to Perfect Healthy Spaghetti Squash Au Gratin
To ensure your Healthy Spaghetti Squash Au Gratin turns out perfectly every time, follow these simple tips.
- Choose ripe squash: Look for a firm, yellowish spaghetti squash without blemishes for the best flavor and texture.
- Don’t skip roasting: Roasting enhances the sweetness of the spaghetti squash, giving depth to the dish.
- Use quality cheese: Opt for sharp cheddar for its robust flavor; it makes all the difference in this gratin.
- Adjust seasoning: Feel free to add more herbs or spices according to your taste. Fresh herbs can elevate the dish further.
- Let it cool slightly: Allowing it to sit for a few minutes after baking helps set the gratin, making it easier to serve.
- Experiment with toppings: Consider adding breadcrumbs or extra herbs on top before baking for added texture and flavor.
Best Side Dishes for Healthy Spaghetti Squash Au Gratin
When serving Healthy Spaghetti Squash Au Gratin, consider these delightful side dishes to round out your meal. Each option complements the gratin beautifully.
- Garlic Bread – A crunchy and buttery side that pairs perfectly with the creamy textures of the gratin.
- Caesar Salad – This classic salad adds crispness and tang, balancing the richness of the au gratin.
- Roasted Vegetables – Seasonal vegetables tossed with olive oil and herbs provide color and nutritional value.
- Quinoa Pilaf – A nutty grain dish that adds a wholesome touch while boosting protein content.
- Steamed Broccoli – Simple and healthy, steamed broccoli offers bright color and nutrients without overwhelming flavors.
- Balsamic Glazed Brussels Sprouts – Their slight bitterness balances out the creaminess of the gratin perfectly.
Feel free to mix and match these suggestions based on your preferences!
Common Mistakes to Avoid
When making Healthy Spaghetti Squash Au Gratin, it’s easy to overlook some details. Here are a few common mistakes and how to avoid them.
- Skipping the roasting step: Roasting spaghetti squash is essential for developing flavor and texture. Don’t rush this part; take the time to roast until tender.
- Overcooking the squash: Ensure you don’t overcook the spaghetti squash as it can become mushy. Test for doneness with a fork; it should be tender but not falling apart.
- Not seasoning adequately: A lack of seasoning can lead to bland flavors. Be generous with salt, pepper, and optional spices like paprika or thyme.
- Using low-quality cheese: The cheese is a key component in achieving that creamy texture. Opt for good quality sharp cheddar for the best results.
- Ignoring cooling time before serving: Allowing the dish to cool slightly helps in setting up and enhances flavors. Serving it too hot may affect its consistency.

Storage & Reheating Instructions
Refrigerator Storage
- Store leftovers in an airtight container.
- Consume within 3-4 days for optimal freshness.
Freezing Healthy Spaghetti Squash Au Gratin
- Place in a freezer-safe container or bag.
- Freeze for up to 2-3 months for best quality.
Reheating Healthy Spaghetti Squash Au Gratin
- Oven: Preheat to 350°F (175°C) and bake covered for about 20 minutes until heated through.
- Microwave: Heat in microwave-safe dish in short intervals, stirring occasionally, until warmed evenly.
- Stovetop: Warm gently in a skillet over medium heat, adding a splash of water or broth if needed.
Frequently Asked Questions
Here are some frequently asked questions about making Healthy Spaghetti Squash Au Gratin.
Can I make Healthy Spaghetti Squash Au Gratin ahead of time?
Yes, you can prepare it a day ahead and store it in the refrigerator. Just reheat before serving.
What can I substitute for Greek yogurt?
You can use sour cream or cottage cheese as an alternative to Greek yogurt while maintaining creaminess.
How do I know when the spaghetti squash is done cooking?
The squash is done when you can easily pierce it with a fork and it shreds into noodle-like strands.
Can I customize the Healthy Spaghetti Squash Au Gratin?
Absolutely! You can add other vegetables like spinach or mushrooms or experiment with different cheeses according to your taste.
Final Thoughts
Healthy Spaghetti Squash Au Gratin is a delightful dish that combines comfort food with wholesome ingredients. Its versatility makes it suitable as both a side dish and a light main course. Feel free to customize it by adding your favorite veggies or spices for an even more personal touch!
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Healthy Spaghetti Squash Au Gratin
- Total Time: 1 hour 15 minutes
- Yield: Serves 6
Description
Indulge in the comforting flavors of Healthy Spaghetti Squash Au Gratin, a delightful dish that combines nutrition and taste without the guilt. This recipe features the lightness of spaghetti squash mixed with creamy Greek yogurt and sharp cheddar cheese, making it a perfect choice for weeknight dinners or special occasions. Its low-carb and gluten-free profile caters to various dietary needs, while its rich flavor from sautéed onions and garlic makes it a crowd-pleaser. Simple to prepare yet satisfying, this dish can be served as a light main course or a hearty side, and it’s easy to make ahead of time for stress-free meal planning.
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 oven to 400°F (205°C).
- Halve spaghetti squash, scoop seeds, brush cut sides with olive oil, and roast face-down on a baking sheet for 35–40 minutes until tender.
- Sauté onions in a skillet with olive oil until softened (about 5 minutes), then add garlic for another minute.
- Shred cooled squash into noodle-like strands.
- Mix shredded squash with sautéed onions and garlic, Greek yogurt, 1 cup cheese, salt, and pepper.
- Transfer to a greased casserole dish, top with remaining cheese.
- Bake at 375°F for 20–25 minutes until bubbly and golden.
- Prep Time: 15 minutes
- Cook Time: 60 minutes
- Category: Main/Casserole
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 serving
- Calories: 210
- Sugar: 3g
- Sodium: 330mg
- Fat: 9g
- Saturated Fat: 5g
- Unsaturated Fat: 3g
- Trans Fat: 0g
- Carbohydrates: 21g
- Fiber: 2g
- Protein: 12g
- Cholesterol: 25mg