There’s something magical about a recipe that brings together comfort and health in one irresistible dish. Spaghetti Squash Au Gratin is exactly that kind of meal—the kind that feels rich and cheesy but is secretly packed with nutritious ingredients. It’s the answer when you’re craving something hearty and cozy but still want to eat clean.

This dish combines tender roasted spaghetti squash with golden sautéed onions and garlic, creamy Greek yogurt, and melty sharp cheddar cheese. The result? A bubbling, slightly crispy-topped casserole that’s just as perfect for a casual weeknight dinner as it is for a holiday spread.

Whether you serve it as a vegetarian main or a cheesy side, it’s bound to be a hit with anyone who takes a bite.

Spaghetti Squash Au Gratin

Why you’ll love this recipe

This recipe checks all the boxes. It’s comforting, satisfying, and filled with flavor, yet still gluten-free, low-carb, and packed with veggies. The squash gives it a hearty, pasta-like feel without any heaviness, and the combination of sautéed garlic, onion, and cheddar cheese is pure flavor magic. It’s quick to prep, adaptable to your dietary needs, and just as good reheated the next day.

Ingredients

(tip: you’ll find the full ingredients and measurements in the recipe card below)

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

Instructions

Preheat the oven to 400°F (205°C). Slice the spaghetti squash in half lengthwise and scoop out the seeds.
Brush the cut sides of the squash with olive oil and place them cut-side down on a baking sheet. Roast for 35 to 40 minutes or until tender.
While the squash is roasting, heat a skillet over medium heat. Add a little olive oil and sauté the diced onions until soft, about 5 minutes. Stir in the garlic and cook for another minute. Remove from heat.
Once the squash is cool enough to handle, use a fork to shred the flesh into noodle-like strands.
In a large mixing bowl, combine the shredded squash, sautéed onion and garlic, Greek yogurt, 1 cup of the shredded cheese, salt, pepper, and optional paprika or thyme.
Transfer the mixture to a greased casserole dish and sprinkle the remaining ½ cup of cheese on top.
Bake at 375°F for 20 to 25 minutes, or until the top is golden and bubbly.
Let the dish cool for 5 to 10 minutes before serving.

Variations

Swap out the cheddar for Gruyère, Monterey Jack, or a blend of cheeses.
Add chopped cooked chicken or crumbled bacon to make it a protein-rich main.
Use dairy-free cheese and coconut yogurt for a vegan twist.
Add chopped spinach, kale, or broccoli for even more veggie power.
Spice it up with red pepper flakes, smoked paprika, or chipotle powder.

Heating and Storage

This dish keeps well and is easy to reheat, making it great for leftovers or meal prep.

To store: Let the dish cool completely, then refrigerate in an airtight container for up to 4 days.
To reheat: Warm individual portions in the microwave or reheat the entire dish in the oven at 350°F until heated through.
To freeze: Transfer to a freezer-safe container after cooling. Freeze for up to 2 months. Thaw in the fridge overnight before reheating.

Frequently Asked Questions

Can I prepare this dish in advance?

Yes, you can assemble the casserole up to a day ahead, cover it, and refrigerate it. When ready to bake, just pop it in the oven and add a few extra minutes to the cooking time.

What’s the best way to shred the spaghetti squash?

After roasting, use a fork to scrape the inside of the squash—it will naturally pull apart into spaghetti-like strands.

Can I make this dish vegan?

Absolutely. Swap the cheddar for a dairy-free cheese and use a non-dairy yogurt or cashew cream in place of Greek yogurt.

How do I prevent the squash from becoming watery?

After roasting, let the squash cool slightly and drain off any excess moisture before mixing it with the other ingredients.

Can I use frozen spaghetti squash?

You can. Just make sure it’s fully thawed and drained before using to avoid a watery casserole.

What cheese works best?

Sharp cheddar is classic and flavorful, but you can try Gruyère for a nutty twist or mozzarella for extra meltiness.

Can I double the recipe?

Yes! Simply double all the ingredients and bake it in a larger dish. You may need to add 5–10 minutes to the baking time.

Is this recipe low-carb?

Yes, it’s naturally low in carbohydrates and fits well into low-carb and keto-friendly eating plans.

What can I serve this with?

It pairs well with roasted meats, grilled chicken, or a fresh green salad for a complete meal.

Can I freeze leftovers?

Yes, this dish freezes well. Cool it completely before freezing in an airtight container. Reheat in the oven for best texture.

Conclusion

Spaghetti Squash Au Gratin is a flavorful, wholesome twist on comfort food that you can feel great about eating. It’s creamy, cheesy, and satisfying, yet it’s made with real, simple ingredients that nourish your body. Whether you’re looking for a hearty side or a lighter main, this recipe brings all the flavor without the heaviness. Make it once and it’s sure to earn a regular spot on your menu.