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A plate of sweet potato and black bean enchiladas.
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4.43 from 7 votes

Butternut Squash and Black Bean Enchiladas

If you are looking for the perfect veggie enchilada recipe then look no further. Butternut Squash and Black Bean Enchiladas are simple to make, using real wholesome ingredients, and are just so delicious! Bake some for now, and freeze some for later. Your future self will thank you!
Prep Time15 minutes
Cook Time45 minutes
Course: Dinner
Diet: Gluten Free
Method: Bake
Author: Lexi's Clean Kitchen


For Enchilada Sauce:

  • 1 tablespoon avocado oil or extra-virgin olive oil
  • 2 tablespoons arrowroot flour
  • 1 tablespoon chili powder 
  • 1 teaspoon salt
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 1/2 teaspoon ground cumin
  • 1 cup tomato sauce
  • 1 tablespoon lime juice
  • 1 cup veggie broth

For Enchiladas:

  • 1 tablespoon avocado oil
  • 1 onion diced
  • 3 garlic cloves minced
  • 2 teaspoons chili powder
  • 1 teaspoon smoked paprika
  • ½ teaspoon cumin
  • ½ teaspoon fine sea salt
  • ¼ cup veggie broth
  • 3 cups finely diced butternut squash about ½ - ¼” diced
  • 2 big handfuls fresh spinach
  • 1 15 ounce can black beans, drained and rinsed
  • 10-14 medium to small tortillas
  • ¾ cup shredded cheddar cheese
  • Cilantro for garnish


  • Preheat oven to 400 degrees
  • Make the enchilada sauce: Heat oil in a small saucepan over medium-high heat. Add the arrowroot flour, chili, salt, garlic powder, onion powder, and cumin and stir together over the heat constantly for 1 minute. Add in the tomato sauce and lime juice, and then gradually add the veggie broth, whisking to remove any clumps. Reduce the heat and let simmer for 5-8 minutes or until the sauce thickens. Taste and adjust seasoning
  • Make the filling: Heat oil in a large pan or dutch oven over medium heat. Add onions and garlic and cook until beginning to soften, about 5 minutes. Add the chili powder, paprika, cumin and salt and cook until fragrant, about 1 minute.
  • Add veggie broth and butternut squash and cook until tender, about 10-15 minutes.
  • Stir in 1 cup of the reserved enchilada sauce, spinach and black beans and cook until the spinach is wilted and the mixture is heated through.
  • Spread ⅓ cup sauce on the bottom of the 9x13 inch (or similar sized) baking dish.
  • Warm tortillas up either in a cast-iron skillet, under the broiler, or in the microwave until malleable. Place 1 tortilla down on a flat surface and fill it with about ½ cup of filling (this amount will vary based on the size of your tortillas). Roll up the tortilla and place it, seam side down in the baking dish. Continue until all of the filling has been used up, about 14 tortillas worth.
  • Pour remaining sauce over the top of the tortillas and sprinkle with cheese.
  • Bake, uncovered in the middle of the oven for 20 minutes. If desired, you can broil the cheese on top for 2-3 minutes at the end.
  • Let the enchiladas rest for 5-10 minutes before serving.
  • Top with cilantro and serve warm with rice, cauliflower rice or side of choice.


For vegan, omit the cheese.
We tested this recipe with corn tortillas and almond flour tortillas (from Siete Foods). Both worked well! The almond flour tortillas got crunchier than expected, so if you using an alternative grain-free tortilla, you might want to cover it for the first half of the bake. Feel free to use whatever tortilla you typically use to make enchiladas here, too. This recipe will fill between 10 and 14 tortillas, depending on the size of the tortillas you use!
To freeze these enchiladas, make sure to assemble them in a freezer-safe container. Fully assemble them, but do not bake. Make sure the filling is completely cool before wrapping in plastic wrap and freezing for up to 3 months. Transfer from the freezer to the refrigerator 12 hours before you plan to bake (also known as the day before you want to eat 'em!) to defrost. Once the food is defrosted bake according to the instructions in the recipe!


Serving: 1/4 recipe | Calories: 726kcal | Carbohydrates: 100g | Protein: 36g | Fat: 18g | Saturated Fat: 7g | Cholesterol: 25mg | Sodium: 555mg | Fiber: 24g | Sugar: 7g