A Healthy Spaghetti Squash Casserole Recipe that is SO easy and delicious. Simple ingredients get baked in the oven for a quick meal everyone will love!
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Spaghetti squash is one of our favorite things to cook with, and using it up in a casserole is just SO delicious!
Many casseroles are loaded with creamy soups or tons of carbs from rice and potatoes. This spaghetti squash casserole is super light and tasty. Lower in carbs, low in fat and protein packed (30g+ per serving!)
This cheesy casserole is the perfect dinner for a busy weeknight or if you’re looking for something to meal prep!
If you like this recipe, you should also try our healthy taco casserole or our stuffed pepper casserole!
Why we love this Spaghetti Squash Casserole Recipe
This spaghetti squash casserole is one of our favorite meals for a few reasons.
- Hearty while being low calorie: This casserole has a super hearty feel to it while still being low calorie. It feels like a classic casserole but is secretly veggie loaded and high in protein
- High Protein: This casserole has over 30g of protein per serving
- Easy to make: You do need to prep the chicken and spaghetti squash but it’s totally worth the extra steps. Beyond that, you just have to mix everything together and bake!
Baked Spaghetti Squash Casserole Ingredients
To make this Casserole you’ll need:
- shredded chicken
- spaghetti squash
- enchilada sauce
- black beans
- cheddar cheese
- diced green chiles
- frozen corn
You can find substitutions for all of these ingredients below in the green shaded substitutions box.
How to Select and Prepare Spaghetti Squash
Selecting a spaghetti squash: Make sure your spaghetti squash is hard and has no soft spots.
Cooking Spaghetti Squash: Here is a post on how to cook spaghetti squash in the microwave and here is a post about how to cook spaghetti squash in the instant pot. Both methods take about 10 minutes.
- Slice spaghetti squash halves and put in your instant pot with 1 cup of water.
- Cover + set pot to sealing for 5 minutes.
- Manually release the pressure + shred your cooked squash with a fork!
P.S. – if you love spaghetti squash, you have to try these 25 Low Carb / Keto Spaghetti Squash Recipes
How To Make Spaghetti Squash Casserole Recipe
- Cook your spaghetti squash and chicken
- In a bowl, add shredded spaghetti squash, enchilada sauce, shredded chicken, beans, corn, and green chiles.
- Mix all ingredients until combined + place in a greased 9×13 oven safe baking dish. Top with cheddar cheese.
- Bake at 400 for 20 minutes until the top starts to brown.
So cheesy and delicious!
Time Saving Tips for Spaghetti Squash Casserole:
To assemble this casserole quickly – cook all the parts ahead of time!
- Spaghetti Squash: Here is a post on how to cook spaghetti squash in the microwave and here is a post about how to cook spaghetti squash in the instant pot. Both methods take about 10 minutes.
- Chicken: You have a few options for shredded chicken. You can make my Easy Instant Pot Shredded Chicken, you can cook the chicken in the crockpot (you’d have to do it the day before or in the morning) OR you can buy a rotisserie chicken and shred it up.. any method will work.
- While your chicken/spaghetti squash is cooking – you can prep the other minimal ingredients, so that you can get it in the oven in no time!
SUBSTITUTIONS FOR SPAGHETTI SQUASH CASSEROLE
Chicken: You can use chicken thighs or even chicken tenders in place of chicken breasts.
Enchilada Sauce: Red or green enchilada sauce will work in this recipe.
Corn: We like to use frozen corn and defrost it but you can also use canned corned (drained and rinse it first!)
Black Beans: Pinto beans or kidney beans would work well in this recipe
Green Chiles: Green chiles are optional but delicious! You can skip them if you don’t have them on hand.
Cheese: You can use pepper jack, monterey jack, or colby jack cheese in place of cheddar. We haven’t tried it with low fat cheese but it would probably work.
Low Salt: If you’re watching your sodium intake look for low salt enchilada sauce and salt free black beans. Cheese is naturally high in salt.
Rice: We have a Best Mexican Chicken Casserole that is similar to this recipe but made with rice if you’re looking for a higher carb meal
Other Flavors: Check out our Buffalo Chicken Spaghetti Squash Casserole or Greek Chicken Spaghetti Squash Bake for other spaghetti squash recipes. We also have a Healthy Chicken Fajita Casserole Recipe
Spaghetti Squash Casserole FAQ
Spaghetti squash doesn’t really taste like spaghetti but it does mimic the texture of it. It’s a great low carb option or perfect for those who have to eat gluten free.
To avoid mushy spaghetti squash make sure to not overcook it. You can also salt the spaghetti squash before cooking it to avoid mushy spaghetti squash. Try to drain the spaghetti squash immediately after cooking it so that you can avoid it absorbing any additional liquid.
Yes you can buy spaghetti squash already cooked or already cut. Most grocery stores sell it. Some stores also sell spaghetti squash cooked and frozen.
Spaghetti squash is a very hearty vegetable. They will last on the counter for at least a month, sometimes longer. You’ll know a spaghetti squash has gone bad when you cut into it and it’s slimy or moldy. Cooked spaghetti squash lasts for about 3-4 days in the refrigerator.
Storing/ Reheating Spaghetti Squash Casserole
Can this recipe be made ahead? Absolutely! I recommend assembling the casserole ahead of time. You can put everything in the dish and leave it in your refrigerator until you are ready to bake. You can also bake it ahead of time and reheat it.
Can this recipe be reheated? Yes, this recipe also tastes great when reheated… Simply reheat in a microwave or in an oven set at 350°F until center is cooked through.
Refrigerator: This casserole will last for up to 3 days in the refrigerator
Freezing: We haven’t tried freezing this casserole. I don’t think it would hold up very well so we don’t recommend it.
Other healthy spaghetti squash recipes:
We love spaghetti squash and have a post with all The Best Keto Spaghetti Squash Recipes if you’re looking for more options. Here are some of our favorite spaghetti squash recipes:
Spaghetti Squash Casserole Recipe
Ingredients
- 1 lb spaghetti squash medium sized, about 2 cups cooked squash
- 2 cups shredded cooked chicken about 1 lb
- 1/2 cup enchilada sauce
- 1 cup frozen corn defrosted
- 1 cup cooked black beans rinsed and dried
- 1 4.5 oz can diced green chiles
- 1 cup shredded cheddar cheese
Instructions
- Preheat oven to 400 degrees + prepare a greased 9×13 oven safe dish
- Fill a microwave safe glass dish with 1 inch of water. Slice spaghetti squash in half + place face down in water. Microwave on high for 10 minutes until cooked OR cook in instant pot following these directions.
- While spaghetti squash is cooking, make shredded chicken. You can cook it in the instant pot, crockpot, or bring a pot of water to a boil on the stove. Cook the chicken in boiling water for 10 minutes + shred (You can also buy a rotisserie chicken + shred!)
- While the chicken cooks, remove spaghetti squash from microwave + shred.
- Once the chicken has cooked, pull it apart with forks to shred.
- In a bowl, add shredded spaghetti squash, enchilada sauce, shredded chicken, beans, corn, green chiles.
- Mix all ingredients until combined + place in a greased 9×13 oven safe baking dish. Top with cheddar cheese.
- Bake at 400 for 20 minutes until the top starts to brown.
- Serve + enjoy!
Sean says
Very easy and delicious. My wife and I started counting our macros this week and this a perfect fit that has all the health benefits we are looking for without giving up any of that delicious taste! Kid approved and back on the schedule again for next week!
The Clean Eating Couple says
So glad you liked it, Sean! Thank you so much!
Crystal says
Super yummy! Tons of flavor but not overwhelming! Definitely a go to dish!
The Clean Eating Couple says
So glad you liked it, Crystal!
Cindi says
This is excellent! I followed the recipe exactly and we loved it! Thank You.
The Clean Eating Couple says
So glad you liked it, Cindi! Thanks!
Ashley Roseberry says
I’m making this tonight. I cooked/shredded the chicken in my IP last night and reserved the broth for soups, etc and I baked my spaghetti squash earlier today. Now all I have to do is assemble! Easy prep-ahead with this recipe! Also, just want to say how much I appreciate a “jump to recipe” link– thank you!!
The Clean Eating Couple says
Thank you so much, Ashley! So glad you enjoyed the recipe and the jump to recipe button – it makes life much easier 🙂
imsen says
I made this for dinner last Wednesday and it was delicious! I’m pretty sure it’s my new favorite way to eat spaghetti squash! 🙂
This was amazing! My husband raved about and asked me to make it again two days later 🙂
Cecelia says
Green chilies come in various can sizes. Please specify can size and serving size. Thank you. Looking forward to making this recipe.
The Clean Eating Couple says
It says it in the recipe!
Danielle K. says
I was surprised at how truly delicious and filling this is! Even my picky kids ate it including the ones who don’t like spaghetti squash. Will definitely make it again!
Patti says
I made this recipe this week- mainly for my 11 month old and I but he loves it so much he takes handfuls and shoves it in his mouth in large scoops haha. Baby and mommy approved- thanks!