Spaghetti Squash Enchilada Boats

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Spaghetti Squash Enchilada Boats are a fun way to enjoy chicken enchiladas while sticking to your goals. This recipe uses a low-carb base filled with a delicious chicken enchilada filling!

549 CAL 54g CARBS 21g FAT 41g PROTEIN 3
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Who said low-carb Chicken Enchiladas have to be boring! I love making chicken enchiladas a little leane by removing the flour tortillas and placing the stuffing inside of roasted spaghetti squash boats. It's a great way to get more veggies and nutrients into your system while still enjoying the juicy chicken and melty cheese goodness of classic enchiladas!

This recipe starts by roasting the spaghetti squash in the oven until it's soft and tender and ready to shred with a fork! Then, you save those strands of squash and mix them with the filling to bulk it up. Then, you make the filling with shredded chicken, sautéed veggies, enchilada sauce, taco seasoning, and black beans and top it with shredded cheese.

The squash is then returned to the oven to melt the cheese until it's bubbly. Top with your favorite toppings, and enjoy a low-carb spin on a Mexican classic!

Spaghetti squash with shredded chicken, black beans, cheese, peppers, onions, and enchilada sauce.

Ingredients You Need to Make This Recipe

Here’s a brief list of what you’ll need to make this recipe:

  • Spaghetti squash: Acts as a healthy, low-carb substitute for pasta. Look for a firm squash that feels heavy for its size.
  • Cooked chicken breast: Shredded chicken adds plenty of protein! You could also use chopped rotisserie chicken, Grilled Chicken Breast, or Mexican Shredded Chicken! Just make sure to omit the red enchilada sauce if you use the latter option since the chicken has some sauce.
  • Taco Seasoning: This mix of spices (or your own blend of chili, cumin, garlic, and onion powders) gives everything a zesty, spicy lift. You can use store-bought or make your own taco seasoning.
  • Red Enchilada Sauce: Feel free to use whatever brand you like. I like to make my own red enchilada sauce, but store-bought works just fine, too.
  • Shredded Mexican cheese: This tops the filling inside the boats for a melty finish. Feel free to use whatever type of cheese you like, such as Monterey jack, cheddar, mozzarella, or pepper jack.

Are these bowls gluten-free?

If you use gluten-free enchilada sauce, then yes, they are gluten-free!

How to Make Enchilada Spaghetti Squash Boats

These boats are so easy to make! Here’s how to do it:

1. Roast the Spaghetti Squash

Preheat your oven and roast the spaghetti squash halves on a baking sheet until they're tender and easy to shred.

2. Start the Filling

Sauté your bell peppers and onions until they're just tender, then toss in shredded chicken, black beans, and taco seasoning.

Halved spaghetti squash with seeds removed, and a pan with shredded chicken, black beans, onions, peppers, and spices.

3. Finish the Filling

Shred the roasted squash into strands and mix it with your sautéed veggies and meat, then stir in some enchilada sauce.

4. Fill the Squash

Fill the squash shells with the mixture, top with extra enchilada sauce and cheese, and bake until the cheese is melted and bubbly.

A bowl of spaghetti squash mixed with chicken, beans, and peppers, and baked spaghetti squash boats topped with melted cheese.

Can I cook the spaghetti squash in the microwave?

Cut your spaghetti squash in half and scoop out the seeds. Place the halves cut side down in a microwave-safe dish with a splash of water. Microwave on high for about 8-10 minutes or until the flesh is tender enough to shred with a fork.

How do I know when the squash is roasted enough?

The squash is ready when the flesh is tender, and you can easily shred it with a fork. If it's still firm in the center, give it a few more minutes in the oven.

A fork lifting a bite of cheesy spaghetti squash enchilada boat topped with sour cream, green onions, and cilantro.

Make This Recipe Your Own

There are so many fun ways to make this recipe your own:

  • Vegetarian: Replace the chicken with extra black beans or add sautéed veggies like zucchini and spinach for a meat-free version.
  • Protein swap: Swap the chicken for ground beef or turkey for a slightly different flavor. Just make sure to cook it first before adding it to the veggies!
  • Spicy: Boost the taco seasoning or toss in some chopped jalapeños or hot sauce for extra heat.
  • Creamy: Stir in a dollop of cream cheese, sour cream, or Greek yogurt to make the filling even richer.
  • Crunchy: Sprinkle crushed tortilla chips or crispy fried onions on top for an extra layer of texture.
  • Taco bowl: Serve the filling in a bowl over rice or with tortilla chips for a fun twist on traditional tacos.
  • Toppings: I used cilantro and green onion, but feel free to add Guacamole, Pickled Red Onions, Pico de Gallo, Salsa Verde, or Habanero Salsa!

What to Serve with Enchilada Boats

You can totally eat these boats on their own or serve them with various sides:

  • Spicy Cabbage and Corn Slaw: The crisp cabbage and sweet corn with a spicy zing add a fresh, tangy crunch that livens up every bite.
  • Healthy Queso Dip: This light, creamy queso drizzles perfectly over your dish, adding a mellow, cheesy note without being too heavy.
  • Mexican Quinoa Salad: Want to add some carbs? This salad is packed with flavor and creamy avocado goodness to balance the main dish!
  • Shortcut Refried Beans: Smooth and savory, these refried beans bring a comforting richness that pairs beautifully with the vibrant flavors of the enchilada squash.

Frequently Asked Questions

Here are the most commonly asked questions about this recipe:

Store your Spaghetti Squash Enchilada in an airtight container in the fridge for up to three days. 

When you're ready to enjoy it, reheat it in the oven at a low temperature to keep the squash tender and the cheese melty, or use the microwave in short bursts, stirring occasionally for even warming. If you're planning ahead, you can assemble the dish a day before and chill it overnight, then add fresh garnishes just before serving.

Spaghetti squash enchilada boats topped with melted cheese, sour cream, and chopped green onions.
The Recipe
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Spaghetti Squash Enchilada Boats

549 CAL 54g CARBS 21g FAT 41g PROTEIN 3
PREP TIME: 10 Min
COOK TIME: 1 Hours
TOTAL TIME: 1 Hours, 10 Min
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Ingredients

US METRICS
  • 2 spaghetti squash (cut in half)
  • 1 red bell pepper, sliced
  • 1 green bell pepper, sliced
  • 1 red onion, sliced
  • 2 cups cooked chicken breast (shredded)
  • 2 cups canned black beans, rinsed and drained
  • 1 tbsp taco seasoning (to taste, or a mix of chili powder, garlic powder, onion powder, cumin, salt, and pepper)
  • 1.5 cups red enchilada sauce
  • 1 cup shredded Mexican cheese (I used reduced fat)
  • 2 tbsp cilantro
  • 2 tbsp green onion, sliced

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Instructions

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1

Preheat the oven to 400 degrees. Cut the spaghetti squash in half and remove the seeds. Lightly spray the squash with cooking spray and sprinkle with salt and pepper. Place cut side down on a baking sheet lined with parchment paper. Roast 35-45 minutes until tender.

2

While the squash cooks, prepare the filling. Heat a skillet over medium-high heat. Add the oil. Once hot, add the peppers and onions. Cook for 6-8 minutes until tender and crisp. Add the chicken, black beans, and taco seasoning. Stir well and cook for about 1-2 minutes. Taste and adjust the seasoning if needed.

3

Once the spaghetti squash is cooked, use a fork to pull it into strands and place it in a large bowl.

4

Toss together the spaghetti squash with the veggie, chicken, and black bean mixture. Toss with about 1 cup of enchilada sauce.

5

Add this mixture back to the empty spaghetti squash halves. Drizzle with extra enchiladas sauce and top with cheese. Bake for 10-15 minutes until the cheese is melted and bubbling. Garnish with cilantro, green onions, and any other enchilada toppings you enjoy.

Equipment

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Nutritional Facts
Serving Size: 1/2 Squash Boat
Amount Per Serving
Calories 549
Calories from Fat 8212
% Daily Value *
Total Fat 21g
1404%
Saturated Fat 9g
47%
Monounsaturated Fat 0g
0%
Polyunsaturated Fat 0g
0%
Cholesterol 97mg
32%
Sodium 1715mg
75%
Total Carbohydrate 54g
18%
Dietary Fiber 15g
62%
Sugars 17g
Protein 41g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

Notes

For a creamy version, add ¼ cup cream cheese, sour cream, or Greek yogurt to the spaghetti squash mixture.
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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
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