Butternut Squash Enchiladas

By Maria Lichty

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Butternut Squash Enchiladas are filled with butternut squash, perfectly spiced black beans, cheese, and enchilada sauce. The perfect vegetarian meal for fall and they freeze well too!

Butternut Squash Enchiladas on plate

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One of my favorite veggies to make during the fall is butternut squash. It has the most delicious, slightly-sweet flavor that makes any dish feel instantly comforting! I love to pair butternut squash with savory black beans for the perfect balance of flavors, and since everyone loves enchiladas…voila! Butternut Squash Black Bean Enchiladas were born. 

As much as my family loves this dish, it’s also fantastic for making and delivering to a friend or neighbor who could use a comforting dish! I would suggest making this recipe in a disposable foil pan, then writing the final baking instructions down for them to finish it and have a warm pan of Butternut Squash Enchiladas ready for dinner.

Butternut Squash Black Bean Enchilada Ingredients

How to Cut a Butternut Squash

For this recipe you’ll need 3 cups of cubed butternut squash. This is about the amount you would get out of a small butternut! If your squash is larger, save the extras for another butternut squash recipe.

Since butternut squash are big and tough a lot of people are intimidated by cutting them, but I promise it’s not hard! 

  • Butternut squash skin is TOUGH! To soften it a bit, you can pierce the skin a couple times with a fork and microwave it for 2 minutes before you get started.
  • Peel the skin off your squash with a vegetable peeler. If you don’t have a good-quality peeler, you can cut the butternut squash in half horizontally, place the flat side down on a cutting board, and slice the skin off with a sharp knife.
  • Cut the peeled butternut squash in half and scoop out the seeds.
  • Now you can dice the squash into cubes! Try to cut them into uniform sizes so they roast evenly across the entire pan.
  • You can cut a butternut squash ahead of time and keep the diced pieces in a sealed container in the refrigerator for 2-3 days prior to cooking.

Roasted Butternut Squash

I like to roast the butternut squash before adding it to the enchiladas because roasting brings out the BEST flavor. Plus, it is so easy!

Drizzle the cubed squash with a little bit of olive oil and season with salt and pepper. Roast until tender, about 20 to 30 minutes.

You can make the filling and prep the rest of the enchiladas while the squash is roasting.

Butternut squash enchilada filling in pan

Homemade Enchilada Sauce

My recipe for Homemade Enchilada Sauce is super easy to make and adds so much flavor. I think it’s way better than store bought and I highly recommend it for this recipe.

I always make extra and keep enough in the freezer to have it on hand for an enchilada night. Of course, in a pinch, your favorite brand of store-bought sauce works great, too.

butternut squash enchiladas in pan


You can use corn or flour tortillas to make the enchiladas. Use your favorite!

Before you start the enchilada assembly line, prep your tortillas so they don’t tear when you roll them full of filling! Wrap tortillas in a damp paper towel and microwave them on high for 30 seconds, flip them over, and microwave for another 30 seconds. You could also briefly fry the tortillas in hot oil!

Enchilada Toppings & Side Dishes

I love to put out the classic toppings when serving up the enchiladas: avocado, sour cream, cilantro, queso fresco, jalapeño slices and lime wedges. It’s a real topping party!

If you are looking for a few side dishes to serve with the enchiladas, here are a few of our favorites:

How to Store Enchiladas

Keep leftovers in an airtight container in the refrigerator for up to five days. Enchilada leftovers are SO good. I even think they are good cold, is that weird? Ha!

Enchiladas also keep really well in the freezer! Freeze for up to three months. This is a great dish to meal prep or make double to have lunches or leftovers ready.

Butternut Squash enchiladas on plate with fork

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Butternut Squash Enchiladas

Butternut Squash Black Bean Enchiladas are a vegetarian classic. Homemade enchilada sauce, roasted butternut squash, perfectly spiced black beans, and cheese are rolled up in tortillas to make one of our favorite fall dinners! Everyone will ask for seconds!
4.59 from 12 votes


  • 3 cups cubed butternut squash
  • 1 1/2 tablespoons olive oil, divided
  • Kosher salt and black pepper, to taste
  • 1/2 red onion, chopped
  • 1 red pepper, stemmed, seeds removed, and chopped
  • 3 garlic cloves, minced
  • 1/3 cup chopped cilantro
  • 1/2 teaspoon ground cumin
  • 1/2 teaspoon chili powder
  • 1/2 teaspoon smoked paprika
  • 15 ounces black beans, rinsed and drained
  • 2 cups red enchilada sauce, I use our homemade sauce
  • 12 corn tortillas, can use flour tortillas
  • 2 cups shredded Monterey Jack or cheddar cheese
  • Garnishes: avocado, jalapeno slices, cilantro, queso fresco


  • Preheat the oven to 400 degrees F.
  • Place the butternut squash cubes on a large baking sheet and drizzle with ½ tablespoon of the olive oil. Toss until well coated. Season with salt and pepper. Roast for 20 to 30 minutes or until tender. Remove from the oven and set aside.
  • While the squash is roasting, heat the remaining 1 tablespoon of olive oil in a large skillet over medium high heat. Add the onion and red pepper and cook until tender, about 5 minutes, stirring occasionally. Add the garlic and cook for one more minute.
  • Stir in the in the cilantro, cumin, chili powder, smoked paprika, and season with salt and pepper. When squash is done cooking, stir in the black beans and butternut squash.
  • Spray a 9×13-inch baking dish with nonstick cooking spray.
  • To assemble the enchiladas, Spread about ¼ cup of the enchilada sauce onto the bottom of the greased baking dish.
  • Wrap the tortillas in damp paper towels and microwave on high for 30-seconds and then flip and heat for 30 more seconds. OR you can briefly fry the tortillas in hot oil. This will prevent them for tearing.
  • Spoon about ¼ cup of the filling in the center of a tortilla. Add a tablespoon of enchilada sauce and a sprinkle of the shredded cheese. Roll each tortilla and place seam side down into the baking dish. Continue the process until filling is gone. It should make 12 enchiladas; but could vary depending on the size of your tortillas.
  • Pour remaining sauce over the top of the filled enchiladas and then sprinkle with remaining shredded cheese, there should be about 1 cup of cheese left for the top.
  • Bake for about 25 to 30 minutes or until cheese is melted and enchiladas are bubbly. Remove the pan from the oven and allow enchiladas to cool for 5 minutes. Garnish with cilantro, avocado, jalapeno slices, and queso fresco, if desired. Serve warm.


Calories: 228kcal, Carbohydrates: 29g, Protein: 10g, Fat: 9g, Saturated Fat: 4g, Cholesterol: 17mg, Sodium: 464mg, Potassium: 343mg, Fiber: 6g, Sugar: 4g, Vitamin A: 4538IU, Vitamin C: 22mg, Calcium: 190mg, Iron: 2mg
Keywords vegetarian

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Photos by Dishing Out Health

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I'm Maria and my husband is Josh. We share a love of cooking, baking, and entertaining. We enjoy creating recipes that are simple, fresh, and family friendly. We love sitting around the table with good food, good conversation, and good friends and family! Our kitchen is always open!
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Vegetarian Fall Winter Kid Friendly Gluten-Free

4.59 from 12 votes (5 ratings without comment)

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  1. 5 stars
    This was truly amazing! My husband, toddler and baby gobbled it right up. I had to use green enchilada sauce for the sake of time, but it worked. Thank you!

  2. 5 stars
    These are delicious. I used different cheeses and chipotle peppers. But, such a lovely blend. Thank you ❤

  3. Great flavors. Add 15-20 to prep time for chopping veggies. Also, cover dish with foil while baking to avoid sauce drying out on tortillas.

  4. 5 stars
    Wow these are good! Even my skeptical nephew loved them. The homemade enchilada sauce totally made this dish. I will never buy sauce again!

  5. 5 stars
    Our family of 4 loved this dish. It tasted great and presented beautifully.

    Three of the four of us enjoy vegetarian cooking, but our youngest likes to have meat.
    So, next time I’ll make two batches and add some roasted chicken in one.

    Thank you!

  6. Hi! I’m making these and didn’t see where you added the Cilantro. Is it just for topping after cooking? Thanks!

  7. 3 stars
    Maybe I used the wrong corn tortillas (already soft) but when I rolled them they fell apart. So I turned the whole thing into a casserole. Am sending to the kids for dinner so won’t know how it will turn out. The filling was great though. Maybe flour torts next time

  8. 5 stars
    I have tried these and they were so yummy. I added poblano pepper and a jalapeno to it and they were so good. I am going to make them again this week. I love butternut squash served in Mexican style dishes. Thank you for the yummy recipe.

  9. 5 stars
    These were delicious and the enchilada sauce was so easy to make!!! I would like to freeze—do you prepare completely (with the sauce and extra cheese on top) and then freeze???