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Baked Spaghetti Squash and Cheese

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This easy, cheesy, Baked Spaghetti Squash and Cheese is a healthier take on mac and cheese! It’s cheesy, loaded with vegetables and feels like comfort food, without the calories and carbs.

Casserole dish of cheesy baked spaghetti squash with green vegetables
Baked Spaghetti Squash and Cheese

I was craving something cheesy, without all the carbs from macaroni and came up with this dish back in 2003. I basically swapped the pasta from my Macaroni and Cheese recipe with roasted spaghetti squash and the results were this wonderful!  The squash takes on a fantastic texture when baked in the cheese sauce.

Bowl of cheesy baked spaghetti squash with green vegetables

Casserole dish of cheesy baked spaghetti squash with green vegetables

Bowl of cheesy baked spaghetti squash with green vegetables

Half of an uncooked spaghetti squash with seeds

How To Make Spaghetti Squash and Cheese

If you’re new to making this winter squash, you don’t have to peel it. Cut the squash in half lengthwise or down the middle for longer strands, scoop out the seeds and bake.

Once the spaghetti squash is done baking and is removed from the shell, there will be a lot of liquid. I recommend wringing it with paper towels or a cheesecloth to avoid this from being too soggy.

You can easily prepare this ahead, then baked just before ready to serve. I reheated leftovers in the microwave for lunch the next day and it was just as good as when I first made it. Great as a main dish or a side.

Spaghetti Squash and Cheese Variations:

  • Try making this with different cheese combos. Try a mix of cheddar and Swiss, or swap it for Havari.
  • Add some breadcrumbs to the Parmesan topping at the end for some texture.
  • Add some cooked chicken sausage for added protein.
  • Make a tuna spaghetti squash casserole buy swapping spinach for tuna and peas

Casserole dish of cheesy baked spaghetti squash with green vegetables

More spaghetti squash recipes you might enjoy:

Baked Spaghetti Squash and Cheese

4.80 from 96 votes
Cheesy baked spaghetti squash and baby spinach – a comforting, cheesy dish, without the guilt. Perfect for Meatless Mondays or any day of the week!
Course: Dinner, Side Dish
Cuisine: American
This easy, cheesy baked spaghetti squash is a healthier take on mac and cheese! It's cheesy, loaded with vegetables and feels like comfort food, without the calories and carbs.
Prep: 10 mins
Cook: 1 hr 35 mins
Total: 1 hr 45 mins
Yield: 7 servings
Serving Size: 1 cup


  • 5 1/2 cups cooked spaghetti squash, from about 2 small see directions below:
  • 1 tbsp butter
  • 1 tbsp olive oil
  • 1/4 cup minced onion
  • 1/4 cup flour, use ap gluten-free flour for GF
  • 2 cups skim milk
  • 1 cup fat free chicken broth, vegetable broth for vegetarian
  • 2 cups 8 oz Sargento 2% reduced fat mild cheddar
  • salt and pepper, to taste
  • 4 cups about 4 oz baby spinach
  • 1/8 cup grated parmesan


  • Preheat the oven to 375ºF.
  • Cut the squash in half lengthwise; remove and discard seeds. Place squash on a baking sheet cut side down. Bake until tender, about 1 hour.
  • Separate the strands of squash with a fork and place in a medium bowl; discard shells. Squeeze out any excess liquid from the squash if watery.
  • Maintain the oven temperature.
  • Heat butter and oil in a large saucepan over medium heat. Add onions and cook about 2 minutes.
  • Stir in flour. Reduce heat to low and cook, stirring continually 3 - 4 minutes.
  • Add milk and chicken broth and continue whisking, raising heat to medium-high until it comes to a boil and becomes smooth and thick, about 2 minutes stirring; season with salt and pepper.
  • Once it becomes thick, remove from heat, add cheddar cheese and mix well until cheese is melted.
  • Adjust salt and pepper to taste, add cooked spaghetti squash and baby spinach, pour into a baking dish and sprinkle parmesan cheese on top.
  • Bake until bubbly and golden 25 to 30 minutes.

Last Step:

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Serving: 1 cup, Calories: 165 kcal, Carbohydrates: 16 g, Protein: 10 g, Fat: 8 g, Saturated Fat: 2 g, Cholesterol: 7.5 mg, Sodium: 278.5 mg, Fiber: 2 g, Sugar: 6.5 g


Two halves of an uncooked spaghetti squash with a spoon scooping seeds out of one half

A cooked half of a spaghetti squash in a bowl with a fork removing the squash strands from the shell
A bowl of creamy spaghetti squash with pieces of spinach

Photo credit: A Beautiful Plate

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641 comments on “Baked Spaghetti Squash and Cheese”

  1. I have made this recipe several times because it is so great and perfect as is. However, I just tried making it with roasted garlic. Also, I only had one spaghetti squash, so I decided to add roasted cauliflower as well. Let me tell you! These additions/substitutions are game changers! Wow!

  2. I return to this recipe regularly, it’s one I’m really grateful for while I try to lose weight because it tastes comforting in a higher-calorie sort of way. My husband and daughter are both fans as well.

  3. This dish was literally the best thing I’ve tasted! It took a long time, but it was so worth it! The longest part was leaving it in the oven, which allowed me to do things around the house so it was perfect!!

  4. We loved this for dinner last night! I wound up with a lot more than 5-1/2 cups of squash, but there was enough sauce to cover it all. I got eight servings out of it, so there was plenty leftover. Absolutely perfect recipe!

  5. This is so yummy, although 2 tbsp. of fat (the butter and olive oil) is not nearly enough for 4 tbsp of flour. I would recommend using 2 tbsp of oil and 2 tbsp of butter so that the flour can properly blend with the fats. I added roasted broccoli instead of spinach – delish!