Healthy Spaghetti Squash Au Gratin
If you’re looking for a dish that feels like a warm hug on a plate, then this Healthy Spaghetti Squash Au Gratin is just what you need! It’s one of my favorite recipes because it perfectly combines comfort food with wholesome ingredients. This dish is not just rich and cheesy; it’s also low-carb, gluten-free, and packed with veggies. Whether you’re whipping it up for a busy weeknight dinner or serving it at a family gathering, this recipe will surely impress everyone at the table.
What I love most about this Healthy Spaghetti Squash Au Gratin is how simple it is to prepare. The roasted spaghetti squash mingles beautifully with sautéed onions and garlic, creamy Greek yogurt, and sharp cheddar cheese. It bakes up golden and bubbly, making it an inviting centerpiece for any meal.
Why You’ll Love This Recipe
- Easy to Make: With just a few simple steps, you can create a delicious dish without spending hours in the kitchen.
- Family-Friendly Appeal: This recipe is a hit with kids and adults alike. Cheesy goodness always wins hearts!
- Make-Ahead Convenience: You can prepare the mixture ahead of time and pop it in the oven when you’re ready to serve.
- Versatile Dish: This healthy au gratin works well as a side dish or a light main course. Perfect for any occasion!

Ingredients You’ll Need
To make this Healthy Spaghetti Squash Au Gratin, you’ll need some simple and wholesome ingredients that are easy to find. Here’s what you’ll gather:
For the Base
- 1 medium spaghetti squash
- 1 tbsp olive oil
- ½ cup diced onion
- 2 cloves garlic (minced)
For the Creamy Mixture
- ½ cup plain Greek yogurt (or sour cream)
- 1½ cups shredded sharp cheddar cheese (divided)
- ¼ tsp salt
- ¼ tsp black pepper
Optional Seasoning
- ¼ tsp paprika or dried thyme
Variations
This recipe is wonderfully flexible, allowing you to customize it based on your preferences! Here are some fun ideas:
- Add Extra Veggies: Toss in some sautéed spinach or mushrooms for added nutrition and flavor.
- Change Up the Cheese: Swap sharp cheddar for mozzarella or pepper jack if you like a little kick.
- Make It Creamier: For an even richer texture, mix in some cream cheese along with the Greek yogurt.
- Top with Breadcrumbs: For added crunch, sprinkle some whole-grain breadcrumbs on top before baking.
How to Make Healthy Spaghetti Squash Au Gratin
Step 1: Roast the Spaghetti Squash
Preheat your oven to 400°F (205°C). Slice the spaghetti squash in half lengthwise and scoop out the seeds. Brushing the cut sides with olive oil helps achieve that roasted flavor we all love. Place the squash face-down on a baking sheet and roast for about 35–40 minutes until tender. This step brings out its natural sweetness!
Step 2: Sauté Onions and Garlic
While your squash is roasting, heat a skillet over medium heat. Sauté the diced onions in a bit of olive oil until they soften—this usually takes about 5 minutes. Adding minced garlic afterward enhances the aroma and taste of your dish. Remove from heat once fragrant!
Step 3: Shred the Squash
Once your roasted spaghetti squash has cooled enough to handle, take a fork and shred its flesh into noodle-like strands. This step transforms your squash into that perfect pasta alternative while keeping everything light!
Step 4: Combine All Ingredients
In a large bowl, mix together those lovely shredded strands of squash with your sautéed onions and garlic, Greek yogurt, 1 cup of shredded cheese, salt, pepper, and optional paprika or thyme. Each ingredient adds layers of flavor that will come together beautifully.
Step 5: Bake Until Golden
Transfer this flavorful mixture into a greased casserole dish. Top with the remaining half cup of shredded cheese—because who doesn’t love extra cheese? Bake at 375°F for about 20–25 minutes until bubbly hot with a delightful golden top.
Step 6: Serve & Enjoy
Let cool slightly before serving so you don’t burn your tongue on that cheesy goodness! This Healthy Spaghetti Squash Au Gratin makes an excellent side dish or can shine as a light main course all on its own. Enjoy every bite!
Pro Tips for Making Healthy Spaghetti Squash Au Gratin
This dish is not only delicious, but with a few expert tips, you can make it even better!
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Choose a ripe squash: Selecting a firm spaghetti squash with a uniform color ensures you’ll get the best flavor and texture. Look for one that feels heavy for its size.
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Don’t rush the roasting: Allowing the squash to fully roast enhances its natural sweetness and provides a better base for your gratin. Check for doneness by inserting a fork; it should easily pierce through.
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Mix up the cheese: While sharp cheddar is fantastic, consider blending in other cheeses like mozzarella or gouda for added richness and flavor complexity.
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Experiment with herbs: Fresh or dried herbs such as parsley, rosemary, or basil can add extra depth to your dish. They not only enhance flavor but also bring in vibrant colors.
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Let it rest after baking: Allowing the gratin to cool slightly before serving helps it set up nicely and makes it easier to scoop out without falling apart.
How to Serve Healthy Spaghetti Squash Au Gratin
Presenting your Healthy Spaghetti Squash Au Gratin can elevate your meal experience! Here are some ideas on how to serve this delightful dish:
Garnishes
- Chopped fresh parsley: A sprinkle of bright green parsley adds a fresh touch and contrasts beautifully with the cheesy layers.
- Crushed red pepper flakes: For those who enjoy a little heat, adding crushed red pepper flakes gives an exciting kick to each bite.
- Sliced green onions: These offer a mild onion flavor that complements the dish while providing a pop of color.
Side Dishes
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Steamed broccoli: Tender broccoli florets add nutrients and balance out the rich flavors of the gratin. Simply steam until bright green and serve alongside.
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Simple mixed greens salad: A light salad with arugula, cherry tomatoes, and a lemon vinaigrette offers freshness that pairs wonderfully with the cheesy squash.
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Roasted Brussels sprouts: Crispy roasted Brussels sprouts bring an earthy flavor and crunchy texture that contrasts nicely with the softness of the gratin.
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Garlic bread: For those craving comfort food, some warm garlic bread makes for an indulgent side that complements the meal perfectly.
Enjoy creating this cozy dish and don’t hesitate to experiment with different pairings and garnishes to make it your own!

Make Ahead and Storage
This Healthy Spaghetti Squash Au Gratin is perfect for meal prep! You can easily make it ahead of time, store leftovers, or even freeze portions for later. Here’s how to keep it fresh and delicious.
Storing Leftovers
- Allow the dish to cool completely before storing.
- Transfer leftovers to an airtight container.
- Refrigerate for up to 3-4 days.
Freezing
- Let the dish cool completely before freezing.
- Portion into freezer-safe containers or bags.
- Label with the date and freeze for up to 2-3 months.
Reheating
- Thaw in the refrigerator overnight if frozen.
- Preheat your oven to 350°F (175°C) and reheat in a covered dish for about 20 minutes or until heated through.
- You can also reheat individual portions in the microwave for 1-2 minutes, stirring halfway through.
FAQs
If you have questions about this recipe, you’re in the right place! Here are some common inquiries from fellow home cooks.
Can I use a different cheese in Healthy Spaghetti Squash Au Gratin?
Absolutely! While sharp cheddar gives a great flavor, feel free to experiment with other cheeses like mozzarella or gouda for a different twist.
How do I know when my spaghetti squash is cooked?
Your spaghetti squash is ready when it’s tender and easily pierced with a fork. It should also be golden on the outside after roasting—just how we like it!
Is Healthy Spaghetti Squash Au Gratin suitable for meal prep?
Yes! This recipe is perfect for meal prep. You can make it ahead, store leftovers, or even freeze portions for later enjoyment.
Can I add other vegetables to Healthy Spaghetti Squash Au Gratin?
Definitely! Feel free to add sautéed spinach, bell peppers, or mushrooms to enhance the veggie goodness and flavor profile.
What can I serve with Healthy Spaghetti Squash Au Gratin?
This versatile dish pairs wonderfully with salads, grilled chicken, or as part of a cozy vegetarian meal spread. Get creative!
Final Thoughts
I hope this Healthy Spaghetti Squash Au Gratin becomes a cherished recipe in your kitchen! Its comforting flavors and nutritious ingredients make it special for any occasion. Enjoy making this delightful dish, and don’t hesitate to share your experience. Happy cooking!
Healthy Spaghetti Squash Au Gratin
Indulge in the comforting flavors of Healthy Spaghetti Squash Au Gratin, a dish that brings together wholesome ingredients with a cheesy twist. This delightful recipe features roasted spaghetti squash mixed with sautéed onions and garlic, creamy Greek yogurt, and sharp cheddar cheese, resulting in a golden, bubbly masterpiece that’s both low-carb and gluten-free. Perfect for weeknight dinners or family gatherings, this versatile dish can be enjoyed as a side or a light main course.
- Prep Time: 15 minutes
- Cook Time: 60 minutes
- Total Time: 1 hour 15 minutes
- Yield: Serves 6
- Category: Main
- Method: Baking
- Cuisine: Vegetarian
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: paprika or dried thyme
Instructions
- Preheat oven to 400°F (205°C). Halve the spaghetti squash, remove seeds, brush cut sides with olive oil, and roast face-down on a baking sheet for 35–40 minutes until tender.
- In a skillet over medium heat, sauté diced onions in olive oil for about 5 minutes; then add minced garlic and cook until fragrant.
- Shred the cooled spaghetti squash into noodle-like strands using a fork.
- In a large bowl, combine shredded squash with sautéed onions and garlic, Greek yogurt, 1 cup of shredded cheese, salt, pepper, and optional seasoning.
- Transfer mixture to a greased casserole dish. Top with remaining cheese and bake at 375°F for 20–25 minutes until bubbly and golden.
- Let cool slightly before serving.
Nutrition
- Serving Size: 1 cup (210g)
- Calories: 185
- Sugar: 3g
- Sodium: 250mg
- Fat: 10g
- Saturated Fat: 5g
- Unsaturated Fat: 4g
- Trans Fat: 0g
- Carbohydrates: 15g
- Fiber: 3g
- Protein: 10g
- Cholesterol: 25mg