Healthy Spaghetti Squash Au Gratin
If you’re looking for a dish that feels indulgent yet is packed with wholesome goodness, then you’ll adore this Healthy Spaghetti Squash Au Gratin! It’s one of those recipes that I turn to time and again, especially when I want something comforting without the guilt. The creamy blend of roasted spaghetti squash, savory sautéed onions, and sharp cheddar cheese creates a delightful harmony of flavors. Plus, it’s perfect for everything from busy weeknights to family gatherings—everyone will be asking for seconds!
This recipe is not only easy to whip up but also showcases the versatility of spaghetti squash in a way that even non-vegetable lovers can appreciate. You’ll love how this dish brings everyone together around the table!
Why You’ll Love This Recipe
- Quick Preparation: This dish comes together in just about 15 minutes of prep time, making it perfect for busy evenings.
- Family-Friendly Flavor: With its cheesy goodness and comforting texture, everyone in the family will enjoy it—even the picky eaters!
- Make-Ahead Option: Prepare it ahead of time and pop it in the oven when you’re ready to serve. Great for meal prep!
- Healthy Comfort Food: Enjoy all the comfort without any of the guilt—it’s low-carb and gluten-free!

Ingredients You’ll Need
You’ll find that making this Healthy Spaghetti Squash Au Gratin is both simple and satisfying. The ingredients are wholesome and easy to gather, ensuring you have everything needed for a deliciously cozy meal.
- 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 Healthy Spaghetti Squash Au Gratin recipe is its flexibility! Feel free to mix things up based on your taste preferences or what you have on hand.
- Add some greens: Toss in some fresh spinach or kale for an extra boost of nutrients.
- Spice it up: Add crushed red pepper flakes for a bit of heat if that’s your style!
- Change up the cheese: Experiment with different types of cheese like mozzarella or gouda for unique flavor twists.
- Include protein: Mix in cooked chicken or turkey for a more filling main dish.
How to Make Healthy Spaghetti Squash Au Gratin
Step 1: Roast the Spaghetti Squash
Preheat your oven to 400°F (205°C). Start by slicing the spaghetti squash in half lengthwise and scooping out the seeds. Roasting brings out its natural sweetness while giving it that tender texture we love. Brush the cut sides with olive oil and place them face-down on a baking sheet. Roast for about 35–40 minutes until tender; you’ll know it’s done when the flesh easily shreds into strands.
Step 2: Sauté Onions and Garlic
While your squash is roasting, heat a skillet over medium heat. Sauté diced onions in a bit of olive oil until they soften—this should take about 5 minutes. Adding minced garlic for just one more minute will fill your kitchen with an irresistible aroma. This step enhances their flavors, making them sweeter and more aromatic.
Step 3: Shred the Squash
Once your roasted squash has cooled enough to handle, grab a fork and start shredding! You’ll want to create those lovely noodle-like strands that make this dish so special. This process gives us that signature spaghetti squash texture, which pairs beautifully with our creamy mixture.
Step 4: Combine All Ingredients
In a large bowl, combine your shredded squash with sautéed onions and garlic, Greek yogurt, 1 cup of shredded cheddar cheese, salt, pepper, and any optional spices like paprika or thyme. Mixing these ingredients together creates a rich filling packed with flavor!
Step 5: Bake It Up
Transfer your mixture into a greased casserole dish and top it off with the remaining half cup of cheese. Baking at 375°F for about 20–25 minutes will create that golden bubbly topping we all crave! Let it cool slightly before serving so those flavors meld perfectly.
Now you’re ready to enjoy this delightful Healthy Spaghetti Squash Au Gratin as either a comforting side dish or as a light main course!
Pro Tips for Making Healthy Spaghetti Squash Au Gratin
Cooking can be a wonderful adventure, and with these tips, you’ll create a delightful dish that will impress your family and friends!
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Choose the Right Squash: Look for a spaghetti squash that feels heavy for its size and has a consistent yellow color. A fresher squash will yield better texture and flavor.
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Don’t Rush the Roasting: Allowing the squash to roast until tender is crucial. This enhances its natural sweetness and ensures it shreds easily into perfect noodle-like strands.
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Experiment with Cheese: While sharp cheddar adds great flavor, feel free to mix in other cheeses like Monterey Jack or pepper jack for a delightful twist. Each cheese brings its unique taste to the dish.
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Customize Your Seasonings: The optional paprika or thyme can be swapped with your favorite herbs and spices! Consider adding some fresh basil or oregano for an extra layer of flavor.
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Make It Ahead: You can prepare the spaghetti squash mixture ahead of time and store it in the fridge for up to 2 days. Just add the cheese topping before baking for an easy weeknight meal!
How to Serve Healthy Spaghetti Squash Au Gratin
Serving this dish is all about making it look as good as it tastes. With a few thoughtful touches, you can elevate your presentation and complement its flavors perfectly.
Garnishes
- Fresh Herbs: Sprinkle chopped parsley or chives on top just before serving for a pop of color and freshness.
- Crushed Red Pepper Flakes: If you enjoy a little heat, a sprinkle of crushed red pepper flakes adds zest and visual appeal.
Side Dishes
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Garlic Roasted Broccoli: Toss broccoli florets with olive oil, garlic, salt, and pepper, then roast until crispy. This dish complements the creamy gratin beautifully while adding extra nutrients.
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Simple Green Salad: A mixed green salad with lemon vinaigrette provides a refreshing contrast to the rich flavors of the au gratin. Toss in cucumbers and cherry tomatoes for added crunch.
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Quinoa Pilaf: Fluffy quinoa cooked with vegetable broth and mixed with herbs makes for a hearty side that pairs well with the cheesy goodness of the gratin.
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Sautéed Spinach: Lightly sauté spinach with garlic until wilted. This quick side adds vibrant color and an extra boost of vitamins without overwhelming your main dish.
Enjoy crafting your perfect plate! Whether it’s for a cozy night in or a festive gathering, this Healthy Spaghetti Squash Au Gratin will surely delight everyone at your table.

Make Ahead and Storage
This Healthy Spaghetti Squash Au Gratin is perfect for meal prep, making it easy to enjoy throughout the week. You can whip up a batch ahead of time and store it for a quick, delicious meal whenever you need it.
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 casserole cool completely before freezing.
- Cover tightly with plastic wrap and then aluminum foil, or use a freezer-safe container.
- Freeze for up to 2-3 months.
Reheating
- Thaw in the refrigerator overnight if frozen.
- Reheat in the oven at 350°F (175°C) for about 20-25 minutes until heated through.
- Alternatively, use the microwave in short intervals until warm.
FAQs
Here are some common questions about this recipe.
Can I make Healthy Spaghetti Squash Au Gratin ahead of time?
Absolutely! You can prepare this dish a day in advance and store it in the fridge. Just bake it when you’re ready to serve!
How do I store leftovers of Healthy Spaghetti Squash Au Gratin?
Leftovers can be stored in an airtight container in the fridge for up to 3-4 days. Just make sure it’s cooled down first!
Can I use different types of cheese in Healthy Spaghetti Squash Au Gratin?
Yes! While sharp cheddar adds great flavor, you can experiment with other cheeses like mozzarella or gouda for a unique twist.
Is this dish gluten-free?
Yes! This Healthy Spaghetti Squash Au Gratin is naturally gluten-free, making it a great option for those with gluten sensitivities.
Final Thoughts
This Healthy Spaghetti Squash Au Gratin is not just a recipe; it’s a warm embrace on a plate! It’s full of flavor, comfort, and nutrition—perfect for any occasion. I hope you enjoy making this dish as much as I do. Share it with family and friends, or savor it all by yourself; either way, you’re in for a treat. Happy cooking!
Healthy Spaghetti Squash Au Gratin
Indulge in a delightful and guilt-free dish with this Healthy Spaghetti Squash Au Gratin. Perfect for busy weeknights or family gatherings, this creamy casserole features roasted spaghetti squash combined with savory sautéed onions, garlic, and sharp cheddar cheese. It’s a comforting yet nutritious meal that even the pickiest eaters will love. With its low-carb and gluten-free profile, this gratin not only satisfies cravings but also brings everyone together around the table. Easy to prepare and customizable, it’s sure to become a staple in your home cooking repertoire!
- Prep Time: 15 minutes
- Cook Time: 1 hour
- Total Time: 1 hour 15 minutes
- Yield: Serves approximately 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: ¼ tsp paprika or dried thyme
Instructions
- Preheat oven to 400°F (205°C). Slice spaghetti squash in half and scoop out seeds. Brush with olive oil and place cut-side down on a baking sheet. Roast for 35-40 minutes until tender.
- In a skillet over medium heat, sauté diced onions in olive oil for about 5 minutes. Add minced garlic and sauté for an additional minute.
- Once the squash is cool enough to handle, shred it into strands using a fork.
- In a large bowl, mix shredded squash with sautéed onions, garlic, Greek yogurt, 1 cup of cheddar cheese, salt, pepper, and optional spices.
- Transfer mixture to a greased casserole dish. Top with remaining cheese and bake at 375°F (190°C) for 20-25 minutes until bubbly and golden.
Nutrition
- Serving Size: 1 cup (240g)
- Calories: 290
- Sugar: 5g
- Sodium: 450mg
- Fat: 16g
- Saturated Fat: 8g
- Unsaturated Fat: 7g
- Trans Fat: 0g
- Carbohydrates: 27g
- Fiber: 6g
- Protein: 14g
- Cholesterol: 35mg