Spaghetti Squash Casserole

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Creamy and comforting, this Spaghetti Squash Casserole makes a perfect keto side dish. Easy and cheesy, with tons of flavor, it turns your dinner into a hearty meal.

Spaghetti Squash Casserole in a white oval baking dish with a striped grey napkin.

I had an absolute bumper crop of spaghetti squash from my garden this year. We grew a variety called stripetti with pretty green stripes, and we weren’t expecting that much out of it. It far exceeded our expectations.

And now we have so many, we need to find ways to use it up. So I am dreaming up as many spaghetti squash recipes as I can! And this creamy, cheesy Spaghetti Squash Casserole is one such recipe.

Oh boy, is it ever good. So hearty and flavorful, this might be my new go-to side dish for fall. At least until I work through all those squash. And with only 5.6g net carbs per serving, it fits the keto diet perfectly.

I may have eaten the leftovers for breakfast too. It goes perfectly with a fried egg and a few slices of bacon. Just saying!

Make sure to try my Twice Baked Spaghetti Squash too. It’s another of my favorites!

Ingredients you need

Top down image of the ingredients for Keto Spaghetti Squash Casserole.

Spaghetti squash: You will need a medium-size spaghetti squash for this recipe, which should be about 3 pounds in weight when whole. It will yield about 4 cups cooked squash.
Sour cream: Sour cream gives the casserole a thick and creamy consistency.
Garlic: I recommend using fresh garlic for the best flavor. You can use pre-minced, jarred garlic instead. If all you have is garlic powder, try using 1 teaspoon.
Italian seasoning: This dried seasoning blend pairs perfectly with the squash and cheese.
Shredded cheese: I used a mild cheddar for the filling and mozzarella for the top of the casserole, plus some Parmesan to play up the Italian flavor. But you can use other cheese as well. Fontina or gruyere would be lovely.
Eggs: The eggs help bind the stringy squash together and give it a more coherent consistency.
Basil: Fresh basil adds both color and flavor.
Kitchen staples: Butter, salt, pepper, red pepper flakes

Step by step directions

A collage of four images showing how to make Spaghetti Squash Casserole.

1. Pre-cook the squash: Cut the spaghetti squash in half, crosswise, and scoop out the seeds. Place cut-side down on the prepared baking sheet and bake at 375ºF for 45 to 60 minute, or until the squash can be squeezed.

2. Scoop out the flesh: Remove and let cool for a few minutes, then scoop the flesh of the squash into a large bowl. Add the butter and let melt.

3. Mix the filling: Add the sour cream, garlic, Italian seasoning, salt, pepper, and red pepper flakes, and stir to combine. Then stir in the eggs, cheddar, and half of the Parmesan until well combined.

4. Sprinkle with cheese and bake: Spread in the prepared baking pan and top with the mozzarella and the remaining Parmesan. Bake at 350ºF for 30 to 35 minutes, until bubbly and browned.

Stripetti squash - a variation of spaghetti squash.

Expert tips

I like to use a large heavy duty spoon for scooping out the seeds of the spaghetti squash. The flesh is quite tough when raw, so a flimsy spoon can easily bend under the pressure.

If your squash is larger than 3 pounds and yields more than 4 cups of cooked flesh, just save the rest for another use. You can refrigerate it for 4 or 5 days, or freeze it for up to 2 months.

Make it a meal!

Turn this spaghetti squash casserole from a side dish into a full meal. Try adding some cooked Italian sausage, ground beef, or cubed chicken to the filling. Then top with cheese and bake as directed.

A spoon digging into a dish of Spaghetti Squash Casserole.

Frequently Asked Questions

Can I eat spaghetti squash on keto?

Spaghetti squash is a good option for keto and low carb diets, but some moderation is required. 1 cup of cooked spaghetti squash has 10g of carbs and 2.2g of fiber, so it’s a little higher in carbs than summer squash like zucchini. So it’s good to be mindful of how much you consume in one sitting.

Should spaghetti squash be hard to cut?

The rind of spaghetti squash is very tough and hard to cut through. Make sure you use a very large, sharp knife and cut on a stable surface. Once you get through the first part of the rind, you will find it easier to cut through the rest. Cutting the squash in half crosswise is also easier than cutting lengthwise, as it’s a shorter distance.

How many carbs are in spaghetti squash casserole?

This creamy spaghetti squash casserole has only 6.7g of carbs per serving and 1.1g of fiber. That amounts to 5.6g net carbs per serving.

A serving of keto Spaghetti Squash Casserole on a white plate with a sprig of basil.

Make Ahead and Storage Tips

If you want to get a jump on meal prep, this Spaghetti Squash Casserole is an ideal make-ahead side dish. You can roast the squash several days in advance, and just keep it in the fridge until you’re ready to assemble.

Or you can bake the full casserole and store it in the fridge for up 5 days, or the the freezer for up to two months. Make sure to wrap it up tightly to avoid freezer burn. Let it come to room temperature before warming it through in the oven.

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