Spaghetti Squash Enchilada Casserole (with Chicken!)

If you have tried my Italian Style Spaghetti Squash Casserole, you will love this recipe for my spaghetti squash enchilada casserole with chicken! It is baked to perfection, with the homemade paleo enchilada sauce from my cookbook, tons of veggies, and homemade refried beans! The ultimate family favorite meal that is great for meal prep, too. Made in partnership with Tuttorosso Tomatoes!

Spaghetti Squash Enchilada CasseroleSpaghetti Squash Enchilada Casserole (with Chicken!)

This Enchilada casserole is the ultimate gluten-free casserole! When I think of casseroles I think of cream cheese, bread or pasta, and all sorts of unhealthy add-ins. Not anymore! Made with the very loved paleo enchilada sauce from my cookbook, loads of veggies, shredded chicken, homemade refried beans, and spaghetti squash, this dish has so much flavor and makes for great leftovers!

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!

Spaghetti Squash Enchilada CasseroleHow to Make A Spaghetti Squash Casserole

This is an amazing dinner, my friends. Everyone who has tried it absolutely loves it. A huge hit all around!

How to Roast Spaghetti Squash

  1. Preheat oven to 375ºF and line a baking sheet with foil or parchment paper.
  2. Cut spaghetti squash in half, lengthwise.
  3. Scoop out seeds.
  4. Brush inside with oil.
  5. Place facedown on baking sheet and adding water to the baking sheet.
  6. Bake for 45-50 minutes, or until you can pierce with a fork.
  7. Simply scrape out “spaghetti” with a fork and Enjoy!

How to Cook Spaghetti Squash in the Instant Pot

  1. Cut spaghetti squash lengthwise and scoop out seeds.
  2. Add 1 cup of water to the Instant Pot.
  3. Stack the spaghetti squash on top of each other (cut-side up).
  4. Close the lid and make sure the knob is turned to sealing.
  5. Set to manual high-pressure for 6-8 minutes (based on size of your squash)
  6. When the timer goes off, turn the vent on the top of the lid to venting to release the steam.
  7. Once the venting knob has dropped, open the lid and shred the spaghetti squash with two forks to turn squash into spaghetti-like noodles!

Spaghetti Squash Enchilada Casserole

Watch the video:

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

Spaghetti Squash Enchilada Casserole

Spaghetti Squash Enchilada Casserole (with Chicken)

Prep Time 10 minutes Cook Time 1 hour 10 minutes Serves 6

Ingredients

Directions

  1. Cook The Spaghetti Squash:  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 notes to cook in the Instant Pot!
  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 refried beans: Heat oil in a medium saucepan over medium-high heat. Add in garlic and spices and let cook until fragrant, about 1-2 minutes. Drain the liquid from the beans and rinse well, then add the beans to the saucepan. Turn down heat and stir well. Add in lime juice and water. Simmer for 1-2 minutes. Take off heat and mash well using a potato masher or fork. Set aside until ready to use. Reduce the heat and let simmer for 10 minutes or until the sauce thickens.
  4. 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. Use immediately or let cool and store in a closed container in the refrigerator for up to 2 weeks.
  5. 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.

Recipe Notes

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

How to Cook Spaghetti Squash in the Instant Pot:

  1. Cut spaghetti squash lengthwise and scoop out seeds.
  2. Add 1 cup of water to the Instant Pot.
  3. Stack the spaghetti squash on top of each other (cut-side up).
  4. Close the lid and make sure the knob is turned to sealing.
  5. Set to manual high-pressure for 6-8 minutes (based on size of your squash)
  6. When the timer goes off, turn the vent on the top of the lid to venting to release the steam.
  7. Once the venting knob has dropped, open the lid and shred the spaghetti squash with two forks to turn squash into spaghetti-like noodles!
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There may be affiliate links in this post! By clicking on them, or purchasing recommended items I may receive a small compensation, at no cost to you! However, I only recommend products I absolutely love and use in my own home! Thank you for supporting Lexi's Clean Kitchen when you shop! See my disclosure policy for more info!

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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31 comments on “Spaghetti Squash Enchilada Casserole (with Chicken!)

  • 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!

    Reply
  • 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.

    Reply
  • 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!

    Reply
  • 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?

    Reply
  • 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.

    Reply
  • 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.

    Reply
  • 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!!!

    Reply
  • Leisha Vogl says:

    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

    Reply
  • 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

    Reply
  • 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

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

    Reply
  • 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

    5.0 rating

    Reply
  • 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.

    5.0 rating

    Reply

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