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Cheesy Spaghetti Squash Bake


This cheesy, comforting Cheesy Spaghetti Squash Bake 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 bake in a glass casserole dish

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.

scooping out a serving of spaghetti squash bake from a glass baking dish

Comforting Casserole

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

Kids love it because it’s energy-dense and delicious. So do I! It also makes a lot of food, so it’s perfect if you need to feed a crowd. Or enjoy the leftovers yourself.

Pair this casserole with grilled chicken, fish, or hard-boiled eggs for protein, and a side of fresh fruit, for a super tasty, balanced meal.

baking dish with spaghetti squash bake and a bowl of it on the side

How to Make Cheesy Spaghetti Squash Bake

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 squashes 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 squashes 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 cream sauce.

a glass bowl full of cooked spaghetti squash

The next part is easy! Saute your garlic, onions, and broccoli in a large pan, then add the flour and broth and heat it until it thickens. 

mixed the sauce of the cheesy spaghetti squash bake

Add a sprinkle of cheese and then bake until bubbly. Enjoy this healthy, tasty, and nourishing dish with your family!

photo of cheesy spaghetti squash bake from overhead.

Cheesy Spaghetti Squash Bake

This cheesy, comforting Cheesy Spaghetti Squash Bake is packed with vitamins and minerals from three different veggies.
3.6 from 126 votes
Print Pin Rate
Course: Main Course
Cuisine: American
Keyword: Spaghetti Squash Bake
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 8 1 cup
Calories: 261kcal


  • 2 medium Spaghetti Squash
  • 3 cup broccoli, florets
  • 1 tablespoon olive oil
  • 1 small onion
  • 2 clove garlic
  • 1/4 cup flour, all-purpose
  • 1 1/2 cup milk
  • 1 cup vegetable broth
  • 1/8 teaspoon salt
  • 1/8 teaspoon black pepper, ground
  • 2 cup cheddar cheese, shredded
  • 1/8 cup Parmesan cheese, grated


  • 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. 
Tried this recipe?Mention @SuperHealthyKids or tag #SuperHealthyKids!


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

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.