Twice Baked Spaghetti Squash and Cheese

All the comforting richness of traditional mac and cheese—made lighter with nutrient-packed spaghetti squash. This Twice Baked Spaghetti Squash and Cheese is a satisfying, cheesy, and wholesome twist on a classic comfort food, perfect for when you’re craving cozy flavors with a veggie-forward approach.

Why You’ll Love This Recipe

This dish gives you the creamy, gooey satisfaction of baked mac and cheese with a fraction of the carbs. The spaghetti squash serves as a delicious, naturally gluten-free pasta substitute, and when paired with a homemade cheddar cheese sauce and golden breadcrumb topping, it becomes an irresistible main or side dish. It’s easy to prepare, comforting, and a creative way to eat more vegetables without sacrificing flavor.

Ingredients

(Tip: You’ll find the full list of ingredients and measurements in the recipe card below.)

• 2 medium spaghetti squash, halved lengthwise and seeds removed

• Olive oil, for drizzling

• 3 tablespoons butter, divided

• 2 tablespoons all-purpose flour

• 1 teaspoon mustard powder

• 2 cups milk (skim, 1%, 2%, or whole)

• 8 ounces sharp cheddar cheese, shredded

• 1 teaspoon salt

• ¼ teaspoon ground pepper

• 1 cup panko bread crumbs (or traditional bread crumbs)

Directions

1. Preheat oven to 375°F and line a baking sheet with parchment paper or foil.

2. Drizzle the cut sides of the spaghetti squash with olive oil and season with salt and pepper.

3. Place squash cut side down on the prepared baking sheet and roast for 45–60 minutes, until fork tender.

4. Allow the squash to cool slightly, then use a fork to shred the flesh into spaghetti-like strands. Set aside and reserve the squash skins for stuffing later.

5. In a large skillet, melt 2 tablespoons of the butter over medium heat.

6. Whisk in the flour to form a paste, then slowly whisk in the milk. Bring to a boil and cook for several minutes, stirring frequently, until thickened.

7. Reduce heat and stir in the shredded cheddar, mustard powder, salt, and pepper until the cheese is fully melted and the sauce is smooth.

8. Add the shredded spaghetti squash to the cheese sauce and mix until fully combined.

9. Divide the cheesy squash mixture evenly back into the 4 squash skins.

10. In a small pan or bowl, melt the remaining tablespoon of butter and stir in the breadcrumbs until evenly moistened.

11. Sprinkle the buttered breadcrumbs on top of each stuffed squash half.

12. Return to the oven and bake for an additional 15 minutes, or until the tops are golden and the filling is bubbling.

13. Serve hot, straight from the squash skins.

Servings and timing

This recipe serves 4 and takes about 1 hour and 15 minutes in total:

• Prep time: 5 minutes

• Bake time (first): 45–60 minutes

• Bake time (second): 15 minutes

Variations

• Add Protein: Mix in shredded rotisserie chicken for a heartier meal.

• Go Gluten-Free: Use a gluten-free flour and breadcrumb alternative for a fully gluten-free dish.

• Spice It Up: Add a pinch of cayenne pepper, crushed red pepper flakes, or a dash of hot sauce to the cheese sauce.

• Mix Cheeses: Swap some of the cheddar with mozzarella, fontina, or gruyère for a melty blend.

• Veggie Boost: Stir in sautéed spinach, kale, or mushrooms to add even more vegetables.

Storage/Reheating

Store leftovers in an airtight container in the refrigerator for up to 4 days. Reheat in the oven at 350°F until warmed through, about 15–20 minutes. To reheat quickly, microwave individual portions for 1–2 minutes, though the breadcrumb topping may lose some crispness. This dish is not ideal for freezing due to the texture of the squash and cheese sauce.

FAQs

Can I make this ahead of time?

Yes. You can prepare the squash and cheese mixture in advance, stuff the skins, and refrigerate. Add breadcrumbs and bake just before serving.

What’s the best way to cut a spaghetti squash?

Use a sharp chef’s knife to carefully cut it lengthwise. Microwave the squash for a few minutes beforehand to soften it slightly if it’s too firm to slice.

Is spaghetti squash a good substitute for pasta?

Yes. While it doesn’t taste like pasta, its texture is similar to noodles and it absorbs sauces well, making it a great low-carb alternative.

Can I use pre-shredded cheese?

You can, but freshly shredded cheese melts more smoothly and makes for a creamier sauce.

How do I know when the squash is done roasting?

It should be fork-tender and easy to shred into strands when fully cooked. Overcooking can make it mushy, so check around the 45-minute mark.

Can I use other types of cheese?

Absolutely. Try mixing in mozzarella, gruyère, or Monterey Jack for different flavor profiles and meltability.

What can I use instead of mustard powder?

You can substitute 1 teaspoon of prepared Dijon mustard for the mustard powder in the cheese sauce.

Can I bake this in a casserole dish instead?

Yes, combine everything and bake in a greased 9×9-inch baking dish. Top with breadcrumbs and bake as directed.

How do I keep the squash from being watery?

Avoid overcooking the squash and let it sit after roasting to release excess moisture before mixing it into the cheese sauce.

Is this kid-friendly?

Yes, the cheesy flavor and fun texture of the squash often appeal to kids, especially when served like mac and cheese.

Conclusion

Twice Baked Spaghetti Squash and Cheese is a clever, delicious spin on traditional comfort food. With gooey cheddar, creamy sauce, and crispy breadcrumbs, it delivers all the satisfaction of mac and cheese—with a nutritious veggie twist. Whether you’re serving it as a main course or a hearty side, this dish is sure to become a favorite at your table.

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