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Spaghetti Squash Casserole


This cheesy, comforting Spaghetti Squash Casserole is packed with vitamins and minerals from three different veggies.

Check out our Ultimate Guide to Spaghetti Squash for tips on cutting and cooking spaghetti squash!

Spaghetti squash and broccoli in a cheesy in a white dish with a green towel beneath

Why Our Kids love Spaghetti Squash

I’ll never forget the first time I served my son spaghetti squash. He was three years old, and we were having an impromptu picnic in the grass. We shared a thermos full of the noodle-y strands topped with homemade beef bolognese, and he scarfed it down happily.

At the time I was surprised he took to this new food. But in retrospect, it makes a lot of sense. Spaghetti squash is as close to pasta as you can possibly get with a fresh vegetable. This alone should make parents of picky eaters clamoring to get their hands on one!

The mild-flavored, carbohydrate-rich veggie also packs in great nutrition. Kids and grownups get plenty of fiber, vitamins, and antioxidants from this fun, familiar-shaped vegetable.

A big scoopful of cheesy butternut squash with broccoli in a serving dish

How to Make Spaghetti Squash Casserole

This cheesy Spaghetti Squash Casserole combines some of my favorite things: fresh vegetables (including broccoli!), creamy cheese sauce, and make-ahead convenience.

The keystone ingredient in this recipe is well-prepared spaghetti squash, and this is the part that you can do up to two days in advance and refrigerate.

I decided to cook my squash in the Instant Pot, which worked great! I cut the squashes in half crosswise, scooped out the seeds, and placed the halves on the trivet above a cup of water. Then I set the manual timer for seven minutes. When the timer beeped, I used the vent to release the pressure all at once (natural release risks mushy squash.).

If you don’t have an Instant Pot, or you’d rather cook your squash the old-fashioned way, you can roast them at 400 degrees for about 30 minutes.

Once your squash is cooked and you’ve pulled out the strands, set them aside while you prepare the cheese sauce.

Start by cooking the onions and broccoli in a large saute pan. Add the flour, milk, and chicken broth and simmer until thick and bubbly. Add the cheese, stir well, add to your spaghetti squash, and bake! If your squash is baked in advance, this casserole comes together pretty quickly.

four process shots of how to make spaghetti squash casserole

Can you freeze Spaghetti Squash Casserole?

The answer is yes! This casserole actually freezes and reheats very well. This recipe makes a fairly large amount, so you can split it into two dishes and freeze one for a future meal. Or, add any extras to individual serving containers and freeze. When covered tightly it should last for up to 6 months in the freezer.

cheesy spaghetti squash casserole in a white serving dish

What to serve with Spaghetti Squash Casserole

Pair this casserole with grilled chicken, fish, or even hard-boiled eggs for protein, and a side of fresh fruit, for a super tasty, balanced meal. We also enjoy this regularly as a vegetarian main dish. It is plenty filling on its own!

spaghetti squash casserole in a serving dish with a large spoon

Looking for more squash recipes?

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3.6 from 258 votes

Cheesy Spaghetti Squash Bake

This cheesy, comforting Cheesy Spaghetti Squash Bake is packed with vitamins and minerals from three different veggies.
Prep Time15 minutes
Cook Time25 minutes
Total Time40 minutes
Course: Main Course
Cuisine: American
Servings: 8 1 cup
Calories: 261kcal



  • Preheat the oven to 375 degrees F.
  • Chop broccoli and onion. Mince garlic.
  • Roast squash or cook in the InstantPot.  Once cooked, scoop the strands of squash with a fork and place in a baking dish. 
  • Heat oil in a saucepan over medium heat. Add onions and garlic and cook about 2 minutes.  Add chopped broccoli and cook until al dente.  Stir in flour. Reduce heat to low and cook, stirring continually 3 – 4 minutes.
  • Add milk and vegetable 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.
  • Pour mixture into the baking dish with the cooked spaghetti squash.  Sprinkle Parmesan cheese on top. Bake for 25 to 30 minutes until golden.



*You can add chicken to this dish to bump up the protein.  Add bite size pieces of uncooked chicken after step 3 and then continue as normal with the recipe. 


Calories: 261kcal | Carbohydrates: 25g | Protein: 11g | Fat: 14g | Saturated Fat: 7g | Cholesterol: 34mg | Sodium: 397mg | Fiber: 4g | Sugar: 10g
Keyword : Spaghetti Squash Bake


Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating


Have you tried this by microwaving with the deep covered baker?
I am going to experiment this weekend , I think this recipe could be a huge time saver and done in less the 30 minutes in the deep covered baker using the microwave!

2 stars
The recipe once done is good but it’s a little bland. I added ground turkey cooked with Italian spices and it really helped. I gave this recipe 2 stars because I felt the I structions were woefully inadequate specifically in step 3. Not sure how long this was supposed to take but it took me an hour and a half.

Any thoughts on what to substitute for the cheese? We are trying to eat whole food plant based and while we love cheese… trying to cut it out. Thoughts?

Hi, looks delicious…. what is the serving size for 31g carbs? My son is type 1 diabetic and takes insulin based off of the carb count for 1 serving size.

I want to leave a comment in case an amateur like myself comes across this. I did wait until after my hangry tears passed to comment.

I did make this tonight. It took me over an hour. And my kids all chose my advice of if you hate it say I love you mom. Thank you for cooking. And making their own meal.

For an amateur cook here is my feedback. For use the microwave to soften the squash please clarify. After 30 minutes I had to Google cook time. It was 10 minutes to get soft enough to shred.

Also “roast the broccoli and squash” is not clear for me. I even asked hubs how to do this and the teen kids who help cook. And we did not know.

My daughter helped with the milk flour segment for 20 minutes and it never thickened. And the ingredients said vegetable stock and instructions say chicken stock.

My meal turned out ok. With an inch pool of liquid in the pan. I never leave feedback. This was the most difficult meal for me by far. But I see this site wants to encourage healthier meals for our kids. So I waited to respond so it can be written for even the novice able to prepare healthier meals.

Made this tonight for my vegetarian daughter and will definitely be making it again for the whole family!
I cut the recipie in 1/2 worked out great and sprinkled Italian/parmesan bread crumbs on top.

Is it ok to use our own phillipines squash .we don’t have that kind of squash here.THANKS

5 stars
Great! Although made some additions. Only had on squash so added an equal amount of brown cooked rice. Also added left over bacon from breakfast 😉

I made this tonight for my mother and I cause we’re the only ones in the family that l like this kind of stuff. I substituted low fat cheese and add some chicken breast chunks and we both enjoyed it.

5 stars
I took one bite of this and literally said “OMG” It is SO good! It tastes like broccoli cheese soup which is a favorite in our house. It’s a total comfort food and perfect for those chilly fall day’s. I will make this again and again! My suggestion to make it less labor intensive is to cook the squash ahead of time. That way it’s cooled for handling when it’s time to prepare the meal.

5 stars
This is absolutely delicious. I usually don’t like spaghetti squash at all but I saw this and thought it looked good and it was! Would absolutely make it again. Served it with marinated chicken breast, Portuguese linguica and rice my family was very happy. Thanks for the great recipie!

5 stars
We made this recipe last night, and it was absolutely delicious. Our whole family LOVED it – including my picky 4 year old. I omitted the pepper from the casserole (because my kids don’t like pepper), but my husband and I added some to our own plates before eating. The flavoring is just right for kids – enough seasoning to be yummy, but not too much to turn kids off of the dish. We added a little more salt, though.

Note to readers: It was a little time consuming to cook the spaghetti squash right before prepping the casserole, but if you can do this ahead of time in an instant pot or in the overn, then let it cool before scooping, it will make your life easier.

5 stars
THIS. WAS. AMAZING!!!!! Only our second time having spaghetti squash, and this was so fabulously tasty! That fact that it is healthy on top it?? Makes it that much more awesome. (Our first recipe had bacon and cheese so not as healthy LOL). I cooked one small to medium squash and halved the recipe. It was fantastic. A definite repeat!!

We haven’t tried it, so I can’t guarantee the results. I would make sure to remove as much moisture from the squash as possible before adding the rest of the ingredients. Let us know how it works for you!

Haven’t made this yet but one question. If I cook whole spaghetti squash in instant pot for a recipe will it taste as good as roasting? I just don’t want to try to cut it raw.

Can I use frozen broccoli or is it best to use fresh? If I use frozen should I do anything differently?

You can use frozen broccoli! Follow the recipe as directed, but instead of cooking with the onions, stir thawed broccoli into the squash mixture before baking.