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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

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Spaghetti Squash Enchilada Casserole

Chicken Enchilada Spaghetti Squash Casserole

5 from 7 votes
Servings 6
Prep Time 10 minutes


  • 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


  • 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.
  • 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.
  • 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.
  • 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: 415kcalCarbohydrates: 56gProtein: 32gFat: 8.7gSaturated Fat: 1.6gCholesterol: 30mgSodium: 300mgFiber: 12.5gSugar: 4g
Course: Dinner
Cuisine: Gluten-free, Paleo, whole30
Author: Lexi

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!

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Recipe Rating


    1. I think it could be frozen after being baked, but there might be some extra water released after reheating due to the spaghetti squash. As long as you don’t mind that, think it could work!

  1. Can It be assembled in the morning, refrigerated and baked for a luncheon that day? Also can I make refried beans night before?

    1. It really depends on the size of the squash you get – I know that’s not a great answer. Roughly 3-4 pound squash would be our best guess.

  2. 5 stars
    Made this a few nights ago for me and my gluten-free husband. Used a couple of shortcuts – leftover refried beans and Frontera red enchilada sauce. It came out great and was different frm the usual Italian style casseroles. It’s a keeper – Thanks!

  3. Going to make tonight. This may be a crazy question but I already bought the squash shredded.. Do I need to warm that up first or just put in the mix as is ? ( I don’t own a microwave)

  4. 5 stars
    Made this last night, and it’s so good! I left out the chicken, and left some of the black beans whole for texture. I used cotija cheese instead of a blend, and served it with lactose free sour cream. It had so much flavor! It’s definitely being added to my regular rotation.

  5. 5 stars
    This was absolutely amazing! I cooked the squash in the Instapot and it turned out perfect. The enchilada sauce was to die for in and of itself. My husband and kids all enjoyed it