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Spicy Butternut Squash Black Bean Enchiladas with Chipotle Greek Yogurt Sauce

Healthy lightened up vegetarian enchiladas with black beans, butternut squash, corn and a delicious chipotle greek yogurt sauce. These enchiladas are packed with protein!
Course Dinner, Gluten Free, Healthy, Vegetarian
Cuisine Mexican
Keyword butternut squash black bean enchiladas
Prep Time 20 minutes
Cook Time 30 minutes
Total Time 50 minutes
Servings 6 servings
Calories 306 kcal
Author Monique of AmbitiousKitchen.com


  • For the sauce:
  • 1 15 oz can good quality tomato sauce
  • 2 chipotle peppers in adobo sauce
  • 3/4 cup nonfat plain greek yogurt
  • 2 cloves garlic, minced or smashed
  • 1 1/2 tablespoons chili powder
  • For the enchiladas:
  • 1 teaspoon olive oil
  • ½ yellow onion, diced
  • 1 clove garlic, minced
  • 4 cups cubed butternut squash (a little over 1 pound)
  • 1 15 oz can black beans, rinsed and drained
  • 3/4 cup fresh or frozen sweet corn
  • Salt and pepper, to taste
  • 2 cups shredded reduced fat Colby jack cheese, plus more if you'd like
  • 12 corn tortillas
  • extra greek yogurt, cilantro, avocado, and green onions, for topping


  1. Preheat oven to 350 degrees F. Spray 9x13 inch baking pan with nonstick cooking spray.
  2. Make the sauce: Add tomato sauce, chipotle peppers with adobo sauce, greek yogurt, chili powder and garlic to bowl of a food processor; process a few times until smooth. Place in the fridge to thicken it up.
  3. Heat olive oil over medium heat in large skillet. Add garlic and diced onions and saute until garlic becomes fragrant (about 1 min). 
  4. Add cubed butternut squash, stir, and cover for about 8 minutes or until fork tender, stirring occasionally to ensure squash doesn't burn. Add a few teaspoons of water to the pan if necessary to help the squash cook. 
  5. Once squash is fork tender, transfer to large bowl and add in black beans, corn, and in 1 cup of prepared enchilada sauce; stir to combine.
  6. To assemble enchiladas: Add 3/4 cup enchilada sauce to bottom of a 9x13 inch pan and spread around. Warm tortillas in microwave for 30 seconds so that they are easier to roll up. If you find them hard to roll, I recommend dipping each tortilla in a bit of the enchilada sauce; this will make it much easier to roll and add flavor, too! 
  7. Add about 1/2 cup of the butternut squash & black bean filling to each tortilla and 1 tablespoon of cheese. Roll each tortilla up and place seam side down in baking pan. Pour remaining enchilada sauce over the top along with remaining cheese.
  8. Bake for 25-35 minutes or until cheese is melted and the edges of tortillas begin to turn a nice golden brown. Top with extra greek yogurt, avocado slices, cilantro, and green onions, if desired. Makes 6 servings – 2 enchiladas each.

Recipe Notes

You usually can find cubed butternut squash at Trader Joe's; it's much easier than cubing it yourself. Also, feel free to use sweet potatoes instead.

Nutrition Facts
Spicy Butternut Squash Black Bean Enchiladas with Chipotle Greek Yogurt Sauce
Amount Per Serving (2 enchiladas)
Calories 306 Calories from Fat 79
% Daily Value*
Fat 8.8g14%
Carbohydrates 46g15%
Fiber 10.5g44%
Sugar 7.4g8%
Protein 16.5g33%
* Percent Daily Values are based on a 2000 calorie diet.