Healthy Spaghetti Squash Au Gratin
If you’re looking for a comforting dish that feels indulgent yet stays true to healthy eating, this Healthy Spaghetti Squash Au Gratin is just the ticket! It combines the heartiness of roasted spaghetti squash with rich flavors from sautéed onions and garlic, creamy Greek yogurt, and sharp cheddar cheese. What I love most about this recipe is how it can fit in seamlessly at any meal—from busy weeknights to festive family gatherings. You’ll feel good serving it, knowing it’s packed with wholesome ingredients.
This dish is a favorite in my home because it strikes that perfect balance between comfort food and nutrition. It’s like a warm hug on a plate that everyone will enjoy.
Why You’ll Love This Recipe
- Easy to make: With simple steps, this dish comes together quickly, making it perfect for any night of the week.
- Family-friendly: Even picky eaters will love the cheesy goodness of this au gratin—trust me!
- Make-ahead option: Prepare it in advance and pop it in the oven when you’re ready to serve, saving you time.
- Versatile side or main: Whether as a cozy side dish or a light main meal, this recipe fits various occasions.

Ingredients You’ll Need
Let’s gather some simple, wholesome ingredients to create this delicious Healthy Spaghetti Squash Au Gratin! You probably have many of these in your pantry already.
- 1 medium spaghetti squash
- 1 tbsp olive oil
- ½ cup diced onion
- 2 cloves garlic (minced)
- ½ cup plain Greek yogurt (or sour cream)
- 1½ cups shredded sharp cheddar cheese (divided)
- ¼ tsp salt
- ¼ tsp black pepper
- Optional: ¼ tsp paprika or dried thyme
Variations
One of the best things about this recipe is its flexibility! Feel free to switch things up based on your taste or what you have on hand. Here are some fun ideas:
- Add more veggies: Toss in some spinach, kale, or even mushrooms for extra nutrients and flavor.
- Change the cheese: Try using mozzarella or pepper jack for a different twist on the classic flavor.
- Make it spicy: Sprinkle in some red pepper flakes or jalapeños if you like a bit of heat.
- Switch up the herbs: Fresh herbs like basil or parsley can bring a bright touch to this dish.
How to Make Healthy Spaghetti Squash Au Gratin
Step 1: Roast the Spaghetti Squash
Preheat your oven to 400°F (205°C). Slice your spaghetti squash in half lengthwise and scoop out those seeds. This roasting step is key; when you cook the squash face-down on a baking sheet for about 35–40 minutes, it becomes tender and easy to shred into those delightful noodle-like strands.
Step 2: Sauté Onions and Garlic
While the squash is roasting, heat a skillet over medium heat. Add a drizzle of olive oil and sauté your diced onions until they soften—about 5 minutes should do it! Then add minced garlic and cook for just another minute. This step brings out their natural sweetness and adds depth to your dish.
Step 3: Shred the Squash
Once your spaghetti squash has cooled enough to handle (you don’t want to burn your fingers!), grab a fork and start shredding it into strands. This gives us that wonderful texture we’re after—like little pasta noodles!
Step 4: Combine Ingredients
In a large bowl, mix those fluffy squash strands with your sautéed onions and garlic. Add Greek yogurt, 1 cup of shredded cheese, salt, pepper, and any optional spices you fancy. Stir until everything is well combined; this is where all those flavors meld together beautifully!
Step 5: Bake Your Dish
Transfer your mixture into a greased casserole dish. Top with the remaining half cup of cheese for that gooey finish we all love! Bake at 375°F for about 20–25 minutes until it’s hot and bubbly with that gorgeous golden top.
Step 6: Serve and Enjoy!
Let your Healthy Spaghetti Squash Au Gratin cool slightly before serving—it’ll be so tempting but trust me on this one! This dish makes an excellent side or can stand alone as a light main course. Enjoy every cheesy bite!
Pro Tips for Making Healthy Spaghetti Squash Au Gratin
Making this dish is a breeze, especially with a few handy tips to ensure it turns out perfectly every time!
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Choose the right squash: Look for a spaghetti squash that feels heavy for its size and has a smooth, firm skin. This ensures you’re getting a fresh, tasty base for your gratin.
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Don’t rush the roasting: Roasting the squash until it’s tender is key to achieving that delightful noodle-like texture. If it’s undercooked, you’ll miss out on those perfect strands.
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Use full-fat Greek yogurt: While low-fat options exist, full-fat Greek yogurt gives a creamier texture and richer flavor, making the dish more satisfying without added calories from heavier cream.
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Experiment with cheese: If sharp cheddar isn’t your favorite, feel free to mix in other cheeses like Gruyère or mozzarella. Each cheese brings its own unique flavor profile and can make the dish even more delicious.
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Make it ahead: This dish can be prepared ahead of time! Just assemble it up to the baking step, cover, and refrigerate. When you’re ready to serve, pop it in the oven straight from the fridge—it’s an easy way to save time during busy weeknights or gatherings.
How to Serve Healthy Spaghetti Squash Au Gratin
This Healthy Spaghetti Squash Au Gratin not only tastes amazing but can also be presented beautifully on your dinner table. Here are some ideas on how to serve this comforting dish:
Garnishes
- Fresh herbs: Sprinkle some chopped parsley or chives on top just before serving for a pop of color and freshness.
- A drizzle of olive oil: A light drizzle of high-quality olive oil adds richness and enhances the flavors of the gratin.
Side Dishes
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Garlic Roasted Broccoli: Toss broccoli florets with olive oil and garlic, then roast them until crispy. This side is healthy and adds a nice crunch alongside the creamy gratin.
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Simple Mixed Green Salad: A light salad with mixed greens, cherry tomatoes, and a balsamic vinaigrette complements the richness of the gratin beautifully while adding freshness.
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Quinoa Pilaf: Fluffy quinoa tossed with veggies like bell peppers and peas creates a nutritious side that balances well with the cheesy casserole.
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Roasted Carrots: Glazed roasted carrots bring natural sweetness and vibrant color to your plate, making them an eye-catching addition alongside your au gratin.
Enjoy crafting this beautiful meal that’s not only delicious but also filled with wholesome ingredients!

Make Ahead and Storage
This Healthy Spaghetti Squash Au Gratin is a fantastic dish for meal prep, allowing you to enjoy delicious flavors throughout the week without much fuss. Making it ahead saves time and ensures you always have a nutritious meal ready to go.
Storing Leftovers
- Allow the dish to cool completely before storing.
- Transfer any leftovers to an airtight container.
- Keep in the refrigerator for up to 4 days.
Freezing
- Let the au gratin cool completely before freezing.
- Portion it into freezer-safe containers or bags.
- It can be frozen for up to 3 months; label with the date for reference.
Reheating
- Thaw overnight in the refrigerator if frozen.
- Reheat in the oven at 350°F (175°C) until heated through (about 20-25 minutes).
- Alternatively, reheat in the microwave in short bursts, stirring in between, until warm.
FAQs
Here are some common questions you might have about this recipe:
Can I make Healthy Spaghetti Squash Au Gratin ahead of time?
Absolutely! This dish is perfect for making ahead. You can prepare it entirely and store it in the fridge or freezer for later enjoyment.
What can I serve with Healthy Spaghetti Squash Au Gratin?
It pairs well with a green salad or roasted vegetables for a complete meal. You could also serve it alongside grilled chicken or fish for added protein.
Is there a substitute for Greek yogurt in Healthy Spaghetti Squash Au Gratin?
Yes! If you prefer, you can use sour cream or a plant-based yogurt as alternatives while keeping the creamy texture intact.
How do I know when my spaghetti squash is done roasting?
The squash should be tender and easily pierced with a fork once it’s done roasting. The flesh will also separate into noodle-like strands when scraped with a fork.
Final Thoughts
I hope you find as much joy in making this Healthy Spaghetti Squash Au Gratin as I do! It’s not just about nourishing your body but also creating comforting meals that bring warmth to your table. Enjoy experimenting with this recipe, and don’t hesitate to share it with friends and family. Happy cooking!
Healthy Spaghetti Squash Au Gratin
Indulge in the comfort of Healthy Spaghetti Squash Au Gratin, a delicious and nutritious dish that beautifully combines the tender texture of roasted spaghetti squash with savory sautéed onions, garlic, and creamy Greek yogurt. Topped with gooey sharp cheddar cheese, this recipe is perfect for any occasion, from busy weeknights to festive family gatherings. It’s not just a meal; it’s a warm hug on your plate that everyone can enjoy guilt-free. Packed with wholesome ingredients, this veggie-filled casserole is both satisfying and easy to prepare, making it ideal for families and meal prep enthusiasts alike.
- Prep Time: 15 minutes
- Cook Time: 60 minutes
- Total Time: 1 hour 15 minutes
- Yield: Serves approximately 6 people 1x
- 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
- Optional: spices like paprika or dried thyme
Instructions
- Preheat oven to 400°F (205°C). Cut the spaghetti squash in half lengthwise, scoop out seeds, and roast face-down on a baking sheet for 35–40 minutes until tender.
- In a skillet over medium heat, add olive oil and sauté onion for about 5 minutes. Add minced garlic and cook for another minute.
- Once the squash has cooled slightly, use a fork to shred it into noodle-like strands.
- Mix the shredded squash with sautéed onions and garlic in a large bowl. Stir in Greek yogurt, 1 cup of cheddar cheese, salt, pepper, and optional spices.
- Transfer to a greased casserole dish and top with remaining cheese. Bake at 375°F (190°C) for 20–25 minutes until bubbly and golden.
- Let cool slightly before serving.
Nutrition
- Serving Size: 1 cup (240g)
- Calories: 280
- Sugar: 3g
- Sodium: 450mg
- Fat: 13g
- Saturated Fat: 7g
- Unsaturated Fat: 5g
- Trans Fat: 0g
- Carbohydrates: 28g
- Fiber: 4g
- Protein: 15g
- Cholesterol: 30mg