Healthy Spaghetti Squash Au Gratin
This Healthy Spaghetti Squash Au Gratin is the kind of cozy-meets-clean dish we all need in our back pocket. It’s rich and cheesy, but naturally low-carb, gluten-free, and veggie-packed. Roasted spaghetti squash is tossed with sautéed onions, garlic, creamy Greek yogurt, and sharp cheddar—then baked until bubbly and golden on top. A deliciously simple dinner or side dish that’s big on flavor and perfect for everything from weeknight meals to holiday spreads!
Why You’ll Love This Recipe
- Flavorful Comfort: Enjoy a cheesy, satisfying dish that feels indulgent while being healthy.
- Easy Preparation: With straightforward steps, this recipe is perfect for cooks of all levels.
- Versatile Dish: Serve it as a side or light main course; it’s great for any occasion!
- Nutritious Ingredients: Packed with veggies and protein-rich yogurt, it’s a wholesome choice.
- Low-Carb Delight: Perfect for those looking to reduce carbs without sacrificing taste.
Tools and Preparation
Before diving into the cooking process, gather your essential tools to ensure a smooth experience. Having everything ready will help streamline your prep time.
Essential Tools and Equipment
- Baking sheet
- Skillet
- Casserole dish
- Fork
- Mixing bowl
Importance of Each Tool
- Baking sheet: Ideal for roasting the spaghetti squash evenly while ensuring easy cleanup.
- Skillet: Perfect for sautéing onions and garlic to release their full flavors before mixing.
- Casserole dish: Helps in baking the au gratin mixture uniformly for a delightful 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)
- 1½ cups shredded sharp cheddar cheese (divided)
Seasoning
- 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). Slice the spaghetti squash in half lengthwise and scoop out the seeds.
Step 2: Roast the Squash
Brush the cut sides of the squash with olive oil. Place them face-down on a baking sheet. Roast for 35–40 minutes or until tender.
Step 3: Sauté Onions and Garlic
While the squash roasts, heat a skillet over medium heat. Sauté onions in a bit of olive oil until softened (about 5 minutes). Add minced garlic and cook for an additional minute. Remove from heat.
Step 4: Shred the Squash
Once the squash is cool enough to handle, use a fork to shred it into noodle-like strands.
Step 5: Mix Ingredients Together
In a large mixing bowl, combine shredded squash with sautéed onions, garlic, Greek yogurt, 1 cup of cheese, salt, pepper, and optional paprika or thyme.
Step 6: Prepare for Baking
Transfer the mixture to a greased casserole dish. Top with the remaining ½ cup of cheese.
Step 7: Bake Until Golden
Bake at 375°F (190°C) for 20–25 minutes until hot and bubbly with a golden top.
Step 8: Serve and Enjoy!
Let it cool slightly before serving. This Healthy Spaghetti Squash Au Gratin makes an excellent side dish or light main course!
How to Serve Healthy Spaghetti Squash Au Gratin
This Healthy Spaghetti Squash Au Gratin is a versatile dish that can be enjoyed in various ways. Whether you are serving it as a main course or a side, there are plenty of options to enhance your dining experience.
As a Main Course
- Pair with a fresh green salad for a light and refreshing meal.
- Serve alongside grilled chicken or turkey for added protein.
As a Side Dish
- Complement with roasted vegetables, such as Brussels sprouts or carrots, for a colorful plate.
- Enjoy it alongside baked fish for a healthy and satisfying dinner.
For Meal Prep
- Divide into individual servings for easy reheating during the week.
- Pair with different proteins throughout the week to keep meals interesting.
How to Perfect Healthy Spaghetti Squash Au Gratin
To ensure your Healthy Spaghetti Squash Au Gratin turns out delicious every time, keep these tips in mind.
- Choose ripe spaghetti squash: Look for a firm squash with a deep yellow color. This ensures the best flavor and texture.
- Don’t rush the roasting: Proper roasting brings out natural sweetness. Make sure it’s tender before removing from the oven.
- Use high-quality cheese: Sharp cheddar provides the best flavor. Consider mixing in some mozzarella for added creaminess.
- Experiment with spices: Adding herbs like thyme or paprika can elevate the dish’s taste. Adjust according to your preference.
- Let it rest before serving: Allowing the gratin to cool slightly helps flavors meld together and makes serving easier.
- Store leftovers properly: Keep any leftovers in an airtight container in the fridge to maintain freshness for up to 3 days.
Best Side Dishes for Healthy Spaghetti Squash Au Gratin
Healthy Spaghetti Squash Au Gratin pairs well with many side dishes. Here are some great options to consider:
- Garlic Roasted Broccoli – Toss broccoli florets with olive oil and garlic, then roast until crispy.
- Crispy Sweet Potato Wedges – Cut sweet potatoes into wedges, season, and bake until golden brown for a sweet contrast.
- Simple Arugula Salad – A quick salad made with arugula, cherry tomatoes, and a light vinaigrette adds brightness.
- Herb Quinoa – Cook quinoa and mix it with fresh herbs and lemon juice for a zesty side that complements the gratin well.
- Steamed Green Beans – Lightly steamed green beans add crunch and color without overpowering flavors.
- Sautéed Spinach – Quickly sauté spinach with garlic for a nutrient-packed side that is quick and easy to prepare.
- Mediterranean Chickpea Salad – Combine chickpeas with cucumbers, tomatoes, and olives for a hearty salad that offers great texture.
- Roasted Cauliflower Steaks – Slice cauliflower into thick pieces, season, and roast until tender; this adds an earthy flavor profile.
Common Mistakes to Avoid
Cooking can be tricky, and even the best recipes can go awry if you’re not careful. Here are some common mistakes to avoid when making Healthy Spaghetti Squash Au Gratin.
- Skipping the Roasting Step: Roasting the spaghetti squash is crucial for achieving the right texture. Don’t skip this step; it enhances the flavor and ensures the squash is tender.
- Overcooking the Onions: While sautéing onions, keep an eye on their color. Overcooked onions can turn bitter. Cook them just until they’re softened and translucent for the best taste.
- Using Low-Quality Cheese: The type of cheese makes a difference in flavor and creaminess. Opt for a sharp cheddar to elevate your dish’s profile instead of low-quality alternatives.
- Not Seasoning Properly: Salt and pepper bring out flavors, so don’t neglect them. Taste your mixture before baking to ensure it’s seasoned well according to your preference.
- Forgetting to Let It Cool Before Serving: Allowing the dish to cool slightly helps it set and makes serving easier. If you cut into it too soon, it may fall apart.

Storage & Reheating Instructions
Refrigerator Storage
- Store leftovers in an airtight container.
- Keep in the fridge for up to 3 days.
Freezing Healthy Spaghetti Squash Au Gratin
- Use a freezer-safe container or wrap tightly in plastic wrap.
- Freeze for up to 3 months for best quality.
Reheating Healthy Spaghetti Squash Au Gratin
- Oven: Preheat oven to 350°F (175°C) and bake for about 20 minutes until heated through.
- Microwave: Place in a microwave-safe dish, cover, and heat on high for 2–3 minutes, stirring halfway through.
- Stovetop: Heat gently over low heat in a skillet, stirring occasionally until warmed through.
Frequently Asked Questions
If you have questions about making Healthy Spaghetti Squash Au Gratin, you’re not alone! Here are some common inquiries answered.
What can I substitute for Greek yogurt in Healthy Spaghetti Squash Au Gratin?
You can use sour cream or a dairy-free yogurt alternative. Both will provide creaminess without compromising flavor.
Can I make Healthy Spaghetti Squash Au Gratin ahead of time?
Yes! Prepare everything up until baking, cover it tightly, and refrigerate overnight. Bake when ready to serve.
How do I know when my spaghetti squash is done roasting?
The spaghetti squash should be tender enough to easily pierce with a fork. It should also have a slightly caramelized surface for added sweetness.
Is there a vegan option for Healthy Spaghetti Squash Au Gratin?
Absolutely! Replace cheese with a vegan cheese alternative and use plant-based yogurt or cashew cream for creaminess while keeping it deliciously satisfying.
Can I add other vegetables to this recipe?
Yes! Feel free to incorporate spinach, mushrooms, or bell peppers into the mixture before baking for added nutrients and flavor.
Final Thoughts
Healthy Spaghetti Squash Au Gratin is perfect as both a side dish or light main course. Its creamy texture and cheesy goodness make it incredibly inviting. You can customize this recipe by adding your favorite veggies or spices. Give it a try and discover how delightful healthy eating can be!
Healthy Spaghetti Squash Au Gratin
Healthy Spaghetti Squash Au Gratin is a deliciously comforting dish that combines the wholesome goodness of roasted spaghetti squash with a creamy, cheesy filling. This recipe is perfect for anyone looking to enjoy a low-carb, gluten-free meal without sacrificing flavor. With layers of sautéed onions, garlic, and rich Greek yogurt mixed with sharp cheddar cheese, every bite offers a delightful blend of textures and tastes. Whether served as a main course or as a side dish for special occasions, this veggie-packed au gratin will quickly become a favorite addition to your healthy meal repertoire.
- Prep Time: 15 minutes
- Cook Time: 40 minutes
- Total Time: 55 minutes
- Yield: Serves 6
- 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
Instructions
- Preheat your oven to 400°F (205°C). Cut the spaghetti squash in half lengthwise and remove the seeds.
- Brush the cut sides with olive oil and place face-down on a baking sheet. Roast for 35–40 minutes until tender.
- In a skillet over medium heat, sauté diced onions in olive oil until softened (about 5 minutes). Add minced garlic and cook for another minute before removing from heat.
- Once the squash has cooled slightly, shred it into noodle-like strands using a fork.
- In a mixing bowl, combine shredded squash with sautéed onions, garlic, Greek yogurt, 1 cup of cheese, salt, and pepper.
- Transfer the mixture to a greased casserole dish and top with remaining cheese.
- Bake at 375°F (190°C) for 20–25 minutes until hot and bubbly with a golden crust.
- Let cool slightly before serving.
Nutrition
- Serving Size: 1 serving
- Calories: 180
- Sugar: 3g
- Sodium: 250mg
- Fat: 10g
- Saturated Fat: 6g
- Unsaturated Fat: 3g
- Trans Fat: 0g
- Carbohydrates: 14g
- Fiber: 3g
- Protein: 9g
- Cholesterol: 30mg