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Home » Recipes » Chicken

Chicken Enchilada Spaghetti Squash Boats

By: Kathryn Doherty | Last Updated: Mar 12, 2025 | Published: Jan 16, 2020
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Chicken enchilada spaghetti squash boats are a fun, light and low-carb take on enchiladas but with the same great flavor and saucy, cheesy goodness.Chicken enchilada spaghetti squash with melted cheese in a casserole dish after baking

It has been enchilada week here on the blog.

I started the week off with homemade easy enchilada sauce, which is ready in about 10 minutes and so flavorful!

Then I shared sweet potato black bean enchiladas, which are my favorite vegetarian enchiladas. So tender and flavorful!

Today it’s a different healthy twist on enchiladas with these fun chicken enchilada spaghetti squash boats.

Baked spaghetti squash with chicken enchilada and melted cheese in a casserole dish

They are lightened up but still have all the delicious flavor of enchiladas - plus all the saucy, cheesy goodness too!

(And I know, these are not at all enchiladas. Nor are they anywhere near an authentic enchilada recipe. I get that. This is my fun low-carb twist.)

Also, cheat alert, we’re taking some shortcuts to make this a really easy meal to put together.

We’re gonna cook our spaghetti squash in the microwave to save some time. (It’s my favorite sneaky way to make them fast. I shared all about microwave spaghetti squash last month.)

We’re also using store-bought rotisserie chicken to make life easy. (Though I have notes if you want to use boneless, skinless chicken breasts instead. Or you could use some Instant Pot shredded chicken.)

So you just sauté your onion, add the chicken and some spices, stir in some enchilada sauce and put all of that over top your tender, cooked spaghetti squash halves.

Saucy chicken enchilada mixture warmed in a skilletMicrowave spaghetti squash halves after cooking and being pulled into strands

Cover the whole she-bang with cheese and bake it for a few minutes to get everything warm and melty, and dinner is done!

Such a fun mash-up of flavors with the tender, soft spaghetti squash and the bold enchilada flavor, all topped with melty cheese.

Deliciousness!

Also, these are gluten-free as long as your enchilada sauce is gluten-free. Refer to my homemade recipe and use a gluten-free flour if you want to make it.

This spaghetti squash recipe is also low-carb and can be made whole 30 by skipping the cheese. Though, sorry, sad face to that.

Baked spaghetti squash with chicken enchilada and melted cheese in a casserole dish

Now, I’ve got some notes, tips and substitutions coming up below on how to make this enchilada spaghetti squash. Just tryin’ to be helpful.

If you want to jump on down to the recipe, simply scroll right on through the rest of the text. The recipe card is near the bottom of the page, above the comments section.

Notes on chicken enchilada spaghetti squash boats:

  • The recipe calls for microwaving your spaghetti squash to keep this pretty quick and easy to prep. However, you can certainly roast yours in the oven. You’ll want to prep them in the same way and then place on a baking sheet and bake at 400 for 30-40 minutes, until tender. (The exact time will depend on the size of your squash.)
  • Rotisserie chicken makes this an easy recipe to fix, but you could substitute leftover grilled or roasted chicken.
  • Or if you have boneless, skinless chicken breasts, just dice two small breasts into half-inch pieces and cook along with the onion in the pan, until cooked through. Then proceed with adding the garlic and seasonings and enchilada sauce.
  • I use my homemade enchilada sauce, but you can definitely substitute store-bought. You’ll need just a bit less than a regular 10 oz. sized can.
  • Want extra veggies? You know I support that. Add a few handfuls of fresh baby spinach to wilt down with the chicken mixture.

Close up of a forkful of chicken enchilada spaghetti squash being taken

Other fun add-ins you could include: a can of diced green chilies or a cup of black beans.

Like it spicy?

You can add a diced jalapeño when you sauté the onion or you can opt for Pepper Jack for your cheese. You can also substitute cayenne for the black pepper for some extra heat.

Or you can just drizzle some hot sauce or sriracha on top when serving. (I do this so my kids can have it not spicy and I can add a little kick just to mine.)

Spaghetti squash served on a white plate with a chicken enchilada mixture and melted cheese piled on top

And of course toppings. Totally optional but always fun.

Topping ideas for enchilada chicken spaghetti squash boats:

  • Chopped fresh cilantro
  • Sliced green onions or chives
  • Sliced avocado or a dollop of guacamole
  • Sour cream or Greek yogurt
  • Extra Monterey Jack or cheddar cheese
  • Hot sauce or sriracha

Spaghetti squash served on a white plate with chicken enchilada mix and melted cheese piled on top

I hope you give these a try for a fun twist on enchilada night.

Enjoy and have a great long weekend if you are off on Monday for MLK Jr. Day - I am for the first time in my adult working life! (Though, don't worry, I'm still bringing you a new recipe that day. )

XO,

Kathryn

Baked spaghetti squash with chicken enchilada and melted cheese in a casserole dish
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4.75 from 4 votes

Chicken Enchilada Spaghetti Squash Boats

Chicken enchilada spaghetti squash boats are a fun, light and low-carb take on enchiladas but with the same great flavor and saucy, cheesy goodness.
Prep Time15 minutes mins
Cook Time10 minutes mins
Total Time25 minutes mins
Yield: 2 servings

Ingredients

For the spaghetti squash:

  • 1 medium cooked spaghetti squash
  • ¼ teaspoon kosher salt
  • ¼ teaspoon black pepper

For the chicken enchilada filling:

  • 1 teaspoon extra-virgin olive oil
  • 1 cup diced onion
  • 2 cloves garlic, minced
  • ¾ teaspoon ground cumin
  • ½ teaspoon chili powder
  • ¼ teaspoon kosher salt
  • ¼ teaspoon black pepper (or cayenne for more heat)
  • 2 cups diced rotisserie chicken (see notes)
  • 1 cup red enchilada sauce
  • 1 ½ cups shredded Monterey Jack cheese

Optional toppings:

  • Fresh cilantro, sliced green onions or chives, sliced avocado or guac, sour cream or Greek yogurt, extra shredded cheese, hot sauce or sriracha

Instructions

  • For the spaghetti squash: Cut the the spaghetti squash in half vertically using a very sharp knife.  (You can microwave the squash whole for 2 minutes to help it soften so it’s easier to cut.) Use a spoon to remove the seeds and pulp from each half.
  • Place the squash halves, cut side down, in a microwave-safe dish with about a half-inch of water in the bottom of the dish. A casserole size dish or Pyrex dish is a good choice, just make sure it can fit in your microwave. (See notes below for instructions on how to roast the spaghetti squash in the oven if you'd rather do it that way.)
  • Microwave on high for 10-15 minutes, until the squash is fork tender.
  • Remove from the microwave carefully (use oven mitts - the dish will be hot!) and carefully turn the squash halves over to let cool slightly.
  • Once cool enough to handle, use a fork to gently pull the strands from the sides of the squash. Season the halves with ¼ teaspoon salt and pepper.
  • For the enchilada mixture: While the squash is cooking, preheat the oven to 400. Then make your filling.
  • Heat a large pan over medium heat and add the olive oil. Add the onion and sauté for 5 minutes, until softened. Add the garlic, cumin, chili powder, salt and pepper and cook for another minute.
  • Stir in the chicken and enchilada sauce and mix well. Cook for one more minute, until everything is warmed through. Turn off heat.
  • Add half of the chicken enchilada mixture to each spaghetti squash half. Top each half with about ¾ cup of shredded cheese.
  • Bake the spaghetti squash halves on a sheet pan (covered with aluminum foil for easy clean-up) for 5-10 minutes, until the cheese is melted. Serve hot with desired toppings and enjoy!

Notes

The recipe calls for microwaving your spaghetti squash to keep this pretty quick and easy to prep. However, you can certainly roast yours in the oven. You’ll want to prep them in the same way and then place on a baking sheet and bake at 400 for 30-40 minutes, until tender. (The exact time will depend on the size of your squash.)
Rotisserie chicken makes this an easy recipe to fix, but you could substitute leftover grilled or roasted chicken. Or if you have boneless, skinless chicken breasts, just dice two small breasts into half-inch pieces and cook along with the onion in the pan, until cooked through. Then proceed with adding the garlic and seasonings and enchilada sauce.
I use my homemade enchilada sauce, but you can definitely substitute store-bought. You’ll need just a bit less than a regular 10 oz. sized can.
Want extra veggies? Add a few handfuls of fresh baby spinach to wilt down with the chicken mixture.
Other fun add-ins you could include: a can of diced green chilies or a cup of black beans.
Like it spicy? You can add a diced jalapeño when you sauté the onion or you can opt for Pepper Jack for your cheese. You can also substitute cayenne for the black pepper for some extra heat. Or you can just drizzle some hot sauce or sriracha on top of the squash when serving.

Nutrition

Serving: 1squash half | Calories: 554kcal | Carbohydrates: 21g | Fat: 26g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!

Baked spaghetti squash halves with a chicken enchilada mixture topped with melted cheese and sprinkled with parsley with a text overlay on the photo.

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Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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