Spaghetti Squash Bake
Cheesy, meaty, it’s the perfect combo! This Spaghetti Squash Bake is a perfect weeknight meal. It is gluten free and high in protein as an added bonus. I promise, you will love it!

Spaghetti squash has become such a popular food ever since the keto craze happened. It’s a way to get some healthy carbs into your meals and is supposed to mimic noodles. Now, full disclosure, I don’t get that feeling of eating noodles when I eat spaghetti squash. But I do really love to make it as a healthy meal.
This Spaghetti Squash Bake is by far our family’s favorite way to eat it. It is super cheesy and full of meat sauce. The spaghetti squash offers a nice bite and sweetness to the dish. While it doesn’t give me the noodle vibes, it does satisfy my craving for a hearty comfort meal, just with a healthier spin!
There are quite a few steps to this recipe but mostly everything can be made in advance if you like to meal prep. You could make the squash and meat sauce up in advance and then just whip up the cheese mixture when you go to make it. Super easy!
I love to have everything on hand for a hearty, healthy, and satisfying dish that my whole family will love. Give it a try!

Details and Tips!
First, you have to cook the spaghetti squash. I like to cook mine flesh side down on a pan with a little salt and pepper. You could add any spices here but I keep it simple since the meat sauce and cheese mixture have a lot of flavor.
While the squash is cooking, I make everything else. I start with the meat sauce since that can simmer on the stove. I use two pounds of ground beef just to make this super meaty. I typically will use my favorite homemade jarred marinara sauce to keep it simple but homemade is good too. When looking for marinara, try to find one with no added sugar.
Once the marinara is done, you can move onto the cheese mixture. All you’re going to do here is throw everything for the cheese mixture in a bowl and mix it up really well.
By this time, the spaghetti squash should be done. To check doneness, I just stab it with a fork. If the form pops through the skin and the flesh is tender, you’re set.
Laying this is really up to you. You could definitely throw everything in a 8x8 dish and mix it up, top with cheese, and be bake it. But I like to layer it, mainly because I want that big layer of the cheese mixture! I do two layers of everything, and then a bonus layer of meat sauce and shredded cheese.

What you need!
- Spaghetti squash
- Ground beef
- Marinara sauce
- Cottage cheese
- Egg
- Parmesan cheese
- Mozzarella cheese
- Basil
- Oregano
- Onion powder
- Garlic powder
- Salt
- Pepper
Customize!
If you prefer a saucy meat sauce opposed to a thicker meat sauce, I recommend using one pound of ground beef opposed to two. This will give you a little bit of a saucier sauce. I find jarred marinara to be the best for this because it is a little thicker than homemade sauce. It also saves on so much time!
If you do not like cottage cheese, you can certainly substitute it out for ricotta cheese. That will give you a similar result without the curds.
Explore more!
Spaghetti Squash Bake
Creamy, cheesy, and gluten free! This Spaghetti Squash Bake is the perfect pre-fall dish that I love to make. It is quick to come together and packed with protein.
- 1 spaghetti squash
- salt
- pepper
For the cheese mix
- 1 cup cottage cheese
- 1 egg
- 3/4 cup parmesan cheese (grated or shredded, divided)
- 1 cup mozzarella cheese (shredded, divided)
- 1/2 teaspoon salt
- 1/4 teaspoon pepper
- 1/2 teaspoon onion powder
- 1/2 teaspoon garlic powder
- 1/2 teaspoon oregano
- 1 teaspoon basil
For the meat sauce
- 2 pounds ground beef
- 16 ounces marinara sauce (your favorite)
For the spaghetti squash
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Preheat the oven to 400 degrees.
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Slice the spaghetti squash in half starting at the top and working down to create two ovals. Remove the seeds.
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Sprinkle with salt and pepper.
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Place the spaghetti squash flesh-side down onto a baking sheet and bake for 40 minutes or until the inside of the spaghetti squash is fork tender.
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Set aside to let cool slightly.
For the meat sauce
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While the spaghetti squash is baking, make the meat sauce.
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Brown the ground beef over medium high heat until there is no pink left. About 10 minutes.
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Add in your favorite marinara sauce and let that simmer over low heat while the squash finishes up in the oven.
For the cheese mix
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Once you have the meat sauce simmering, move forward with the cheese mixture.
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In a medium mixing bowl, add in the cottage cheese, egg, 1/2 cup of the mozzarella cheese, 1/2 cup of the parmesan cheese, salt, pepper, onion powder, garlic powder, oregano, and basil.
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Give that a good mix until everything is well incorporated.
For assembling
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Once the spaghetti squash has finished baking, flip it over to release the steam and some of the heat. Let it sit until it is cool enough to handle.
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Remove all of the spaghetti squash from the skin and put it in a bowl.
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In an 8x8 (or similar size) glass dish, put 1 cup of the meat sauce on the bottom, spreading it evenly. Now add 1/2 of the spaghetti squash. Top with 1/2 of the cheese mixture. Repeat these layers one more time. Top the final cheese layer with another cup of the meat sauce and the rest of the mozzarella and parmesan cheese.
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Bake for 30 minutes or until the top is golden brown and the sides are bubbly.
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Let the spaghetti squash bake rest for 15-20 minutes before servings.