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Cheesy Spaghetti Squash Casserole Recipe

This easy baked spaghetti squash casserole is the perfect low carb comfort food! When you’re craving pasta, try this healthy alternative instead. It’s also the perfect weeknight dinner for you and your family. 

Spaghetti Squash Casserole

I find casseroles to be one of my favorite things to make. I love to do all my prep work ahead of time and getting all of my dishes done so I only have 1 thing in my oven. 

This is a great make-ahead recipe that I hope you all love as much as my family does. It fed us for several days and was so easy to make. It’s not only keto-approved but it’s also a plain ole healthy meal that even your kids will eat right up. 

What is Spaghetti Squash Casserole?

This super easy spaghetti squash casserole is made up of a homemade sausage ragu sauce, mixed in with cooked spaghetti squash, topped with gooey mozzarella cheese then baked to perfection. It’s so easy and delicious!! 

Is Spaghetti Squash Low Carb/Keto?

Spaghetti Squash Casserole

Using spaghetti squash instead of pasta is a great overall healthy alternative. But keep in mind spaghetti squash still has some carbs, even though it’s still a great vegetable. Spaghetti Squash itself has about 5.5 Net Carbs for 1 cup.

For 1 serving of our spaghetti squash casserole, there are about 5.7 NET Carbs, for 1/2 cup.

Now you might think that’s a lot, but actually, 1/2 cup of spaghetti squash casserole is pretty filling, plus once you add any meatballs, meat sauce, chicken, veggies, or whatever else to your dish, you will find yourself happy and content. But if you set aside enough carbs for the day then by all means…go in for a second helping! 

Is Spaghetti Squash a “Good” Carb?

Like most veggies, spaghetti squash has carbs but still has so many good health benefits: 

  • low in calories
  • high in Vitamin A – helps your vision and immune system
  • plenty of B Vitamins – breaks down the carbs and turns them into glucose
  • Manganese – a mineral that helps with brain function and your nervous system
  • lots of Vitamin C – helps create collagen to help your skin, nails, and hair
  • Potassium – helps muscle function for our nerves, heart, and kidneys 

What Ingredients are in this Spaghetti Squash Casserole?

Spaghetti Squash Casserole

Spaghetti Squash – The main ingredient to your casserole. I used 1 whole cooked squash, which was about 5-6 cups. 

Sausage – This is my preference since I’m not a huge fan of plain ground beef. But you can use ground beef, turkey, or chicken. 

Tomato Sauce – So I used some homemade tomato sauce that I had stored in the freezer. But you can use any homemade sauce or store-bought. If using store-bought then obviously check the nutrition facts and look for one that doesn’t contain any added sugar. 

Spices – Salt, pepper, Italian seasoning, and garlic powder. You don’t need a lot of each of these spices. But I add them to the sausage while it’s cooking. 

Mozzarella Cheese – I layer the spaghetti squash with the mozzarella cheese then cover the whole top with shredded mozzarella. But if you want fewer calories, then only add some to the top and forget adding it to the middle of your casserole. 

6 Ways to Cook Spaghetti Squash

what is the best recipe for Spaghetti Squash

So there are about 6 different common ways of cooking spaghetti squash. I will briefly go over the 6 ways, but for plenty of more information please check out our blog post How to Cook Spaghetti Squash. It will give you a more detailed explanation of everything you need to know.

Oven Halves – This is the traditional way of cooking spaghetti squash. Basically, you are cutting the squash in half and then roasting it in the oven. This is the most common way and used in many spaghetti squash recipes, especially casseroles.

Oven Whole – If you have never cooked spaghetti squash before or are afraid to cut it, this is your best option. You can roast it whole in the oven and cut it later.

Oven Rings – This is a cool way to cook it on a tray, and one of my personal favorites. If you are in a hurry to eat, this way will also cook a whole bunch faster than baking it whole or in half.

Microwave – Of course everything is quicker in the microwave, and this squash is no exception.

Instant Pot – This method of cooking is new to us but we are finding that things cook so quickly in the instant pot and cook thoroughly too. They are not too expensive and are a good addition to any kitchen.

Slow Cooker – This is a good method for cooking most things while you are at work or busy making other things in your kitchen. It cooks up tender and frees up your hands while doing other things.

How to Make the Best Spaghetti Squash Casserole 

I’ve already said several times how easy this casserole is, but honestly guys it’s a piece of cake! I’ll walk you through it….

Making the Spaghetti Squash

Next we’re going to make the spaghetti squash. Again, please refer to our post on How to Cook Spaghetti Squash for more details, but this will give you an overview on how to do it.

Rinse your spaghetti squash to remove any dirt, then dry it off. Using a large chef’s knife and a cutting board, insert your knife into the squash cutting it in half lengthwise. Be very careful! It can be tricky to cut, just go slowly.

Cutting Spaghetti Squash

Scoop out the seeds from both halves. (You can set the seeds aside if you want and roast them later on. Just rinse the seeds off and put them on a small tray and roast them.)

scooping out Spaghetti Squash seeds

Once the squashes have had their seeds removed, then drizzle some olive oil over the squash, then season with salt and pepper.

coating Spaghetti Squash with olive oil

Flip the squash to be face side down. Roast at 400 degrees for about 40 minutes or so. Keep in mind it might take a little more than 40 minutes, everyone’s ovens are different.

Spaghetti Squash halves cooked in the oven

When the squash is cooked, flip them right side up. As soon as it’s cool enough to handle, then take one half at a time into your hand and with the other hand take a fork and pull out the strands. They should come out really easily.

Spaghetti Squash strings

Transfer the squash to a bowl. 

Making the Meat Sauce

The second step is to make our meat sauce, or as my sister-in-law from Italy says “Ragu.” Don’t worry it’s not the ragu that is sold at your local grocery store, it’s homemade and delicious.

Start by adding your sausage, salt, pepper, Italian seasoning, and garlic powder to a frying pan.

Turn the heat onto medium and brown the sausage until it’s cooked.

Spaghetti Squash Casserole

Once the sausage is fully cooked, add about ⅓ of the tomato sauce, stir together. Once the ragu is all mixed then transfer to a bowl and set aside. 

Putting the Casserole Together

Add about half of the spaghetti squash to the frying pan and pour half of the remaining tomato sauce.

Mix together then add the rest of the spaghetti squash and then the remaining tomato sauce. Toss the squash to make sure it’s covered in sauce.

Spaghetti Squash Casserole

Now add the meat ragu to the squash and toss until it’s mixed in. Sprinkle in about 1 ½ cups of mozzarella and mix together.

Pour the spaghetti squash into your casserole dish, then cover the top with the remaining mozzarella.

Spaghetti Squash Casserole

Bake for about 15-20 minutes at 350 minutes. If the cheese doesn’t get brown turn the broiler on for a few minutes. 

Spaghetti Squash Casserole

There you are, your spaghetti squash casserole is done! Enjoy!

Tips for Making Spaghetti Squash Casserole

Spaghetti Squash Casserole

Here are some extra tips to keep in mind when making spaghetti squash:

  • Spaghetti squash takes about 45-60 minutes to cook in the oven, so keep that in mind when figuring out your timing.
  • Sausage, ground beef, ground turkey, ground chicken can all be used.
  • Replace the meat with sauteed veggies to make this casserole vegetarian. 

Is Spaghetti Squash Supposed to Be Crunchy?

So I actually really like my spaghetti squash a little bit on the crunchy side. Not too much, cause it needs to be soft enough to pull out with a fork. But when it’s slightly crunchy it really keeps the stringy spaghetti texture.

Now you don’t have to have it crunchy if you don’t want, that’s just my personal preference. 

Other Diets this Recipe is Good for

  • This casserole is gluten-free.
  • So this can be made vegetarian by replacing the meat with some sauteed veggies.
  • To make it vegan, take out the meat and leave out the cheese, or get some vegan cheese instead.

Different Variations on Spaghetti Squash Casserole

Spaghetti Squash Casserole

You can add or replace almost anything you want. Heres a few ideas for you:

  • Replace the sausage with ground beef, turkey or chicken.
  • Add veggies such as zucchini, yellow squash, bell peppers, broccoli, etc…
  • Leave out the cheese entirely.
  • Replace the mozzarella with cheddar, parmesan or another cheese of your choice.

What Other Cheeses Can You Use?

I tend to always stick to mozzarella or parmesan when making anything Italian, but that doesn’t mean you have to. 

I’ve heard some people love to use Gouda cheese in there spaghetti squash casseroles, or even a grated fontina would work nicely. 

And like they say….cheddar is always better. But if you have another favorite cheese you want to try, go for it!

What to Serve with Spaghetti Squash Casserole

I served this easy spaghetti squash casserole as our main course for dinner, but if you like to add different sides, there are plenty of options you can serve with spaghetti squash casserole. 

One idea is to throw together an easy green salad and some low carb dinner rolls. Now you have a complete all-around healthy dinner your whole family will enjoy. 

Can I Make it Ahead of Time?

Spaghetti Squash Casserole

Spaghetti squash casserole doesn’t have to be made at the moment, and can absolutely be made ahead of time if you find that more convenient for you.

That’s the best part of this recipe. It can be made the day of or even the day before. All you need to do is follow the recipe card instructions and cover it with foil and keep it in the fridge until you’re ready to bake it. 

How to Store Spaghetti Squash Casserole

Of course, if there are any leftovers (doubtful), you’ll need a way to store them so you can eat them the next day.  No problem, it’s very easy to keep spaghetti squash casserole fresh.

You can transfer the leftover spaghetti squash casserole to smaller containers and keep stored in the fridge. Or depending on how much you have leftover, you can just cover the casserole dish with plastic wrap or foil and then put into the fridge. 

Last time I made it, I just covered the whole casserole dish and scooped it out as needed. I had the room in my fridge for the big casserole dish, and I like to keep down on my use of Tupperware when possible. 

Can I Freeze This Recipe? 

Yes!! Surprisingly this baked spaghetti squash casserole freezes pretty well. Store it in a glass or plastic container and freeze for up to 3 months. When ready to eat, defrost overnight in the fridge and then put it back into the oven to reheat. 

Spaghetti Squash Casserole

Other Low Carb Side Dishes:

If you’re looking for some other Low Carb Sides then try our:

Both of them are low carb and your family and friends will love them!

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Spaghetti Squash Casserole

Cheesy Spaghetti Squash Casserole Recipe

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  • Author: Stephanie Parlegreco
  • Total Time: 75-105 minutes
  • Yield: 12 Servings (1/2 Cup Per Serving) 1x
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This easy baked spaghetti squash casserole is the perfect low carb comfort food! When you’re craving pasta, try this healthy alternative instead. It’s the perfect weeknight dinner for you and your family.


  • 2 cups tomato sauce
  • 1 tsp salt
  • 1 tsp pepper
  • 1 tsp garlic powder
  • 1 tsp Italian seasoning 
  • 3 cups shredded mozzarella
  • 1 lb Italian sausage
  • 6 cups spaghetti squash (1 whole spaghetti squash) 


  1. Preheat the oven to 400 degrees. 
  2. Rinse the spaghetti squash to remove any dirt. Pat dry. Using a large chef’s knife, insert it into the squash cutting it in half lengthwise. Be careful, cut slowly. Once the squash is cut, use a spoon and scoop out the seeds and flesh. 
  3. Drizzle olive oil over the squash and season with salt and pepper. Bake squash face down on a baking tray for about 45-60 minutes.
  4. To make the homemade meat ragu: In a medium frying pan add the sausage, salt, pepper, Italian seasoning, and garlic powder. Sautee until sausage is completely cooked. Add in about ⅓ of the tomato sauce, stir together then transfer to a bowl. Set aside.  
  5. Once the squash is done, take it out of the oven and flip it over. Using a fork, pull squash out making strands. Transfer to the frying pan. 
  6. Pour half of the remaining tomato sauce over the squash, mix together then add remaining squash and sauce. Toss the squash to make sure it’s covered in sauce. Now add the meat ragu to the squash and toss until it’s mixed in. Sprinkle in about 1 ½ cups of mozzarella and mix together.
  7. Transfer the squash to a casserole dish and sprinkle the remaining cheese on top.
  8. Bake for 15-20 minutes until cheese is melted and bubbling. Broil for 2-3 minutes if needed. 


  • 6 different ways to cut spaghetti squash.
  • For the meat ragu, you can use sausage, ground beef, turkey, or chicken.
  • To make it vegan replace the meat with sauteed veggies instead and completely take the cheese out or use vegan cheese.
  • The casserole can be made up to a day ahead of time, keep stored in the fridge until ready to bake.
  • It can be stored in an airtight container then put in the freezer for up to 3 months. Thaw in the fridge before ready to reheat in the oven.
  • Prep Time: 15 minutes
  • Cook Time: 60-90 minutes
  • Category: Side Dishes
  • Method: Baking
  • Cuisine: American
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