Chicken Enchilada Spaghetti Squash Casserole

This Chicken Enchilada Spaghetti Squash Casserole is comfort food lightened up! All the classic flavors of your favorite chicken enchiladas, including refried beans, made healthier with spaghetti squash as its base. This gluten-free and dairy-free meal is the ultimate family favorite meal that is great for meal prep, too. Made in partnership with Tuttorosso Tomatoes!

Spaghetti Squash Enchilada Casserole close upChicken Enchilada Spaghetti Squash Casserole

This Enchilada casserole is the ultimate gluten-free casserole! This healthy and hearty enchilada casserole made with spaghetti squash has all the Mexican flavor you love that is a definite crowd favorite. This recipe has loads of veggies, shredded chicken, homemade refried beans, spaghetti squash and is so comforting.

Here’s what you need to make it:

  • 5 cups cooked spaghetti squash
  • 2 cups shredded chicken (rotisserie chicken or make it)
  • 1 green bell pepper
  • 1 red pepper
  • 1 yellow onion
  • 2 cups spinach
  • 1 batch refried beans (or buy it)
  • arrowroot flour
  • enchilada spices
  • tomato Sauce
  • chicken broth
  • herbs for garnish

Spaghetti Squash Enchilada Casserole

This recipe is made in partnership with my friends at Tuttorosso Tomatoes, my favorite tomatoes that I trust time and time again in my kitchen. Other Tuttorosso favorites include my Lasagna SoupInstant Pot Chicken CacciatorePizza Stuffed Peppers, and One Pan Indian Spiced Chicken and Cauliflower!

Ingredients for enchilada casserole

How to Make this Enchilada Casserole

  1. Roast or cook the squash in an Instant Pot. Check out this article for more info.
  2. Pre-cook and veggies that go with it.
  3. Make the refried beans and sauce.
  4. Assemble and bake!

Cheesy top of casserole with avocado slices

Watch the video:

If you like this recipe, try these other Spaghetti Squash Recipes:

Scoop of enchilada casserole from the oven


Chicken Enchilada Spaghetti Squash Casserole

  • Author: Lexi
  • Prep Time: 10 minutes
  • Cook Time: 1 hour and 10 minutes
  • Total Time: 1 hour and 10 minutes
  • Yield: 6 1x
  • Category: Dinner
  • Cuisine: gluten-free, paleo, whole30


  • 5 cups cooked spaghetti squash
  • 2 cups shredded chicken (rotisserie chicken or make it)
  • 1 green bell pepper, diced
  • 1 red pepper, diced
  • 1 yellow onion, diced
  • 2 cups spinach, loosely packed
  • 1 batch refried beans (or buy it)

Enchilada Sauce:

  • 2 tablespoons avocado oil or extra-virgin olive oil
  • 2 tablespoons arrowroot flour
  • 1 tablespoon chili powder
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 1/2 teaspoon ground cumin
  • 1/2 teaspoon fine sea salt
  • 1/2 cup Tuttorosso Tomato Sauce
  • 1 cup chicken broth

To garnish:

  • Chopped cilantro, for garnish
  • Chopped scallions, for garnish
  • Optional: 1/4 cup Mexican blend cheese, more for topping


  1. If you don’t already have spaghetti squash cooked, start by doing that:  Preheat oven to 375ºF and line a baking sheet with foil or parchment paper. Cut spaghetti squash in half, lengthwise. Scoop out seeds. Brush inside with oil. Place facedown on baking sheet and add 1 tablespoon or so of water to the baking sheet. Bake for 45-50 minutes, or until you can pierce with a fork. Once done, scrape out squash into spaghetti stands and set aside. See this article for more info on cooking spaghetti squash.
  2. While cooking, sauté the veggies: Over medium heat, add 1 tablespoon oil and sauté onions and peppers for 5-8 minutes until soft. Add in spinach and mix to wilt. Set aside.
  3. Make the Enchilada Sauce: In a small saucepan over medium-high heat, heat the oil. Add the arrowroot flour and stir together over the heat constantly for 1 minute. Stir in the chili powder, garlic powder, onion powder, cumin, and salt. Then add the tomato sauce and gradually add the chicken broth, whisking to remove any clumps. Reduce the heat and let simmer for 10 minutes or until the sauce thickens. Taste and adjust any spice as desired.
  4. Assemble and Bake: Preheat oven to 350ºF. In a large bowl combine cooked spaghetti squash, shredded chicken, sautéed veggies, refried beans, enchilada sauce, and optional cheese. Spread evenly into a greased baking dish and top with additional optional cheese. Bake for 20-30 minutes until cheese is bubbly. Garnish and serve.


Omit cheese and beans for dairy-free, paleo, and Whole30-compliant!


  • Calories: 415
  • Sugar: 4g
  • Sodium: 300mg
  • Fat: 8.7g
  • Saturated Fat: 1.6g
  • Carbohydrates: 56g
  • Fiber: 12.5g
  • Protein: 32g
  • Cholesterol: 30mg

Did you make this recipe?

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This post is sponsored by Tuttorosso Tomatoes. All thoughts and opinions are always 100% my own! I love the integrity of their products and think you’ll love them too. Thank you for continuing to support LCK and the brands I work with!

January 10, 2018

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Join The Discussion

40 Responses

  1. Hello this recipe looks delicious however would you be kind enough to list the nutrition breakdown? Thank you, Valerie

  2. Delicious!!! I made this last night and was alittle nervous with all the steps and prep but it ended up being soo easy. I can’t wait to make it again and I had plenty of leftovers to bring for lunch today at work.

    5.0 rating

  3. I made this last night and we love it!!!
    It’s soooo good! Our kids are ages 3, 5, 7 and 9. They don’t usually eat all that well but they loved this soo much and had seconds and thirds. Our 7 year old said “Mom we have to have this all the time!”
    Thank you!!!

    5.0 rating

  4. Sounds amazing! Is this something you could make the night before to through in the oven the next day or will the ingredients become too soggy?

    5.0 rating

  5. Made this today…major snow storm here so I used kale and riced cauliflower because I had no peppers or spinach. My daughter makes happy noises when she eats something good (it is really cute) and she is mmm, mmm, mming as we speak. I was going to skip the beans, but it adds the best layer, and the sauce…OH MY! Such a winner, Lexi…many gold stars for you!!!

  6. Probably my favorite of Lexi’s recipes I’ve made! I omitted the cheese and it was still creamy and delicious! It’s hard to get my husband behind something with this many veggies but he loved it too! I’ll definitley be making it again.

  7. I made this on Friday and it was full of flavor. The enchilada sauce is key to the flavor as it has much more flavor then the canned sauce you would easily substitute when reading the recipe. The refried beans could be substituted with can, but again making them as outlined above added to the flavor. It came together pretty quickly once all the ingredients were ready to go. Using rotisserie chicken makes it easier as this is a longer prep recipe with the sauce and beans but really came together quickly. I did use the optional cheese but it’s really not necessary. Can’t wait to eat the leftovers.

  8. This looks delicious! Does everything need to be hot when assembled for baking or would it be possble to prep some of these components ahead?

  9. Made this last night! It was amazing. Even my boys gobbled it up. I did both squash and chicken in the instant pot. (So easy)! I substituted black beans for the refried because I was running out of time and it’s what I had on hand. I will never buy store bought Enchilada sauce again! So easy and delicious. Looking forward to trying it with the refried beans next time. So yummy!!! Even better the next day with eggs!

  10. Made this tonight. I did the chicken and squash in the Instantpot. It was delicious. I won’t ever need to buy premade enchilada sauce or refried beans again. I was not a spaghetti squash eater before.

  11. So excited for this! Going to try the squash in instant pot. I usually just poke a buncha holes in the squash and bake it whole…easier for me to cut.
    Looks delicious! Just did a chicken on the grill so half-way there!

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