Butternut Squash Enchiladas

Butternut squash enchiladas are a vegetarian dinner dream. The slightly sweet combination of squash combined with the rich, earthy spices of ancho chili powder, cumin, and oregano create a sure-to-please vegetarian take on a classic.

Casserole dish filled with homemade vegetairan enchiladas fillled iwth butternut squash and topped with cheese
Sally Vargas

Butternut squash is to fall as zucchini is to summer: There’s always a lot of it, and a lot to do with it.

This recipe for enchiladas—made with corn tortillas, bathed in a spicy red sauce, and filled with roasted squash—just made my autumn meal plan more exciting! In fact, anything to do with tortillas makes the world go round in my house, so this meal is a guaranteed winner.

Calabaza is the generic name in Spanish for hard squashes that grow south of the border, which are akin to butternut and acorn squash. Though it may not be exactly Mexican (in the same way a butternut squash is not exactly the same as a pumpkin) the use of squash in Mexican cuisine is very common.

Do You Need to Peel Butternut Squash?

Stop right there. I discovered that peeling butternut squash is a matter of taste. If you are pureeing it, I concede that you could peel it. But if you are roasting it? That’s your call. The skins are not unpleasant. They are not even as tough as apple skins. Whether you peel or not, you still have to remove the seeds.

Casserole dish filled with easy vegetarian enchiladas fillled iwth butternut squash and topped with cheese
Sally Vargas

How To Cut a Butternut Squash

  1. The best way to tackle a squash is to separate the “neck” from the bulbous end, and deal with it in two parts with a large chef’s knife.
  2. Once you have cut the neck from the round end, you will have two pieces. Work with one piece at a time. We have a tutorial on how to do that here.
  3. Take the round end and halve it, then scoop out the seeds with a sharp-edged spoon. Place the flat side down on the cutting board, slice it into wedges, and slice the wedges into chunks.
  4. The “neck” is a cylinder. Trim off the stem end, and then trim a thin strip along one side of the cylinder so you have a flat edge of squash. Set the squash so the flat side is down. From there, you can safely cut it into slabs and cut the slabs into cubes.

How To Make Enchilada Sauce

The long way to make enchilada sauce is to roast tomatoes and re-hydrate dried ancho chiles, but the enchilada sauce in this recipe is easy and straightforward.

I took the liberty of using canned tomatoes and pure ancho chili powder (not the generic chili powder which usually has dried onion or garlic and sometimes cumin or other spices) to make it quick and easy. Although I prefer ancho chili powder, if you can’t find it, feel free to use whatever chili powder you have available to you.

Puree all the sauce ingredients in a blender and then cook the sauce in a skillet, which will be convenient when it comes time to dip the tortillas in the sauce. Just a few minutes of cooking brings all the flavors together.

Corn tortilla dipped in enchilada sauce and filled with butternut squash and black beans.
Sally Vargas

What Is the Best Cheese for Enchiladas?

Monterey Jack is a good, melty cheese to go on top of the enchiladas, but you can use a "Mexican" blend, or cheddar if you like. I like the mildness of Monterey Jack, because it lets the sauce shine.

What Are the Best Tortillas for Enchiladas?

Corn tortillas hold their shape better than flour tortillas when dipped in sauce, and they’re gluten-free as well, with lots of corny flavor! They are readily available at most grocery stories, but you can also make corn tortillas from scratch. Here’s our favorite recipe for homemade corn tortillas.

How To Prep Tortillas for Rolling Enchiladas

Lightly frying tortillas in oil before dipping them in sauce is the traditional method of making enchiladas. The oil adds flavor and helps create a barrier between the tortilla and the sauce, so the tortilla doesn’t disintegrate. It also softens them, so you can roll them easily.

Since frying is tedious and messy, I worked out a way to use the microwave, which takes a fraction of the time of pan frying:

  1. Brush the tortillas with oil and stack them on a plate.
  2. Cover with waxed paper and microwave at 30-second intervals, until they are hot and pliable, usually for about one minute total.

I like to do six tortillas at a time, fill them, and repeat with a second stack.

Casserole dish filled with easy vegetarian enchiladas fillled iwth butternut squash and topped with cheese
Sally Vargas

The Best Ways to Top Enchiladas

Choose as many or as few garnishes as you like: Radishes, cilantro, avocados, and chopped onion or scallions are all good. I especially like using Mexican crema (or diluted sour cream, which mimics Mexican crema), to add a touch of creaminess to the enchiladas.

Make-Ahead Tips for Enchiladas

It’s best to make all the components ahead (the sauce, the filling, even the ‘fried’ tortillas), store them separately for up to three days, and then assemble just before baking and serving. The tortillas will need to be reheated if they become stiff.

To freeze the assembled and uncooked pan of enchiladas (including the grated cheese topping), wrap the pan in plastic and then in foil, and freeze for up to two months for optimal freshness.

Remove the plastic, cover loosely with foil, and bake straight from the freezer for 30 minutes; then remove the foil and continue baking until hot all the way through, 20 to 30 minutes longer.

Leftovers will keep in the refrigerator for about three days and can be reheated in the microwave.

Looking for More Great Vegetarian Recipes?

Butternut Squash Enchiladas

Prep Time 45 mins
Cook Time 25 mins
Total Time 70 mins
Servings 6 servings

If want to cut down on some of the preparation time, buy grated cheese and pre-peeled and seeded squash, to be cut into 3/4-inch pieces (you will need 5 to 6 cups).


For the vegetables:

  • 1 (2-pound) butternut squash, seeds removed and cut into 3/4-inch pieces

  • 1 large onion, cut into 8 wedges

  • 2 cloves garlic

  • 2 tablespoons olive oil

  • 1/2 teaspoon kosher salt

  • 1/8 teaspoon black pepper

For the sauce:

  • 1 (28-ounce) whole tomatoes with juice

  • 1 tablespoon ancho chili powder, or regular chili powder

  • 1/2 teaspoon oregano

  • 1/2 teaspoon cumin

  • 1/2 teaspoon kosher salt

  • 1 tablespoon olive oil

For the filling and assembly:

  • About 1/4 cup olive oil, to brush on the tortillas

  • 1 (15-ounce) can black beans, rinsed and drained

  • 12 (7-inch) corn tortillas

  • 2 cups grated Monterey Jack cheese

For the garnishes (optional):

  • 1 handful cilantro leaves

  • 1 avocado, sliced

  • 6 radishes, thinly sliced

  • 1/4 red onion, sliced

  • 1/2 cup sour cream, thinned with milk to the consistency of thick cream


  1. Preheat the oven:

    Preheat the to 450ºF.

  2. Roast the squash, onion, and garlic:

    On a large, rimmed baking sheet, mound the squash cubes in the center and place the onion wedges and garlic on the side.

    Sprinkle everything with the olive oil, salt, and pepper. Toss to coat the vegetables and spread them evenly over the baking sheet, segregating the onion and garlic alongside the squash. Bake for 25 minutes, or until tender.

    Remove the pan from the oven, and reduce the oven temperature to 375°F. Let the squash and onion cool slightly on the baking sheet.

    Butternut squash diced on a cutting board for vegetarian enchiladas.
    Sally Vargas
    Butternut Squash and onions on a roasting pan.
    Sally Vargas
  3. Make the sauce:

    In a blender, combine the tomatoes, chili powder, oregano, cumin, and salt. Add the garlic and half of the roasted onion slices. Puree until smooth.

    In a medium skillet set over medium heat, add 1 tablespoon olive oil. Once the oil shimmers, add the pureed sauce to the pan and bring to a simmer. Cook, stirring often, for 5 minutes. Set aside.

    Onion, chili powder and tomato sauce in a blender.
    Sally Vargas
    Red enchilada sauce in a skillet.
    Sally Vargas
  4. Make the filling:

    Transfer the squash and the remaining onion slices to a bowl. Separate the onion slices. Stir in the drained beans. Taste and add more salt, if you like.

    Butternut Squash and black beans in a bowl for vegetarian enchiladas.
    Sally Vargas
  5. Warm the tortillas:

    Using a pastry brush, brush both sides of each tortilla with oil. Place up to 6 tortillas in a stack on a microwave-safe plate.

    Loosely cover and microwave in 30-second intervals until the tortillas are warm and pliable; this takes about 1 minute.

    Wait to repeat the process with the remaining 6 tortillas until you’ve filled the first batch.

  6. Assemble the enchiladas:

    Spread a thin layer of sauce over the bottom of a 9x13-inch baking dish.

    Dip one tortilla in the sauce and set it on a plate. Place about 1/3 cup of the filling in a line down the center of the tortilla. Sprinkle with about 1 tablespoon of cheese.

    Roll up the tortilla to enclose the filling and set it in the baking dish with the seam side down.

    Repeat until all 12 of the tortillas are filled. Pour the remaining sauce over the enchiladas and sprinkle the remaining cheese on top.

    Corn tortilla dipped in enchilada sauce.
    Sally Vargas
    Corn tortilla dipped in enchilada sauce and filled with butternut squash and black beans.
    Sally Vargas
    Enchilada sauce in the bottom of a casserole dish with a vegetarian enchilada on top.
    Sally Vargas
  7. Bake the enchiladas:

    Bake for 25 minutes at 375°F, or until the cheese melts and the enchiladas are hot all the way through. Serve with the garnishes of your choice.

    Pan of black bean and butternut squash enchiladas.
    Sally Vargas
Nutrition Facts (per serving)
554 Calories
34g Fat
47g Carbs
20g Protein
Show Full Nutrition Label Hide Full Nutrition Label
Nutrition Facts
Servings: 6
Amount per serving
Calories 554
% Daily Value*
Total Fat 34g 44%
Saturated Fat 12g 61%
Cholesterol 48mg 16%
Sodium 945mg 41%
Total Carbohydrate 47g 17%
Dietary Fiber 12g 41%
Total Sugars 7g
Protein 20g
Vitamin C 27mg 136%
Calcium 431mg 33%
Iron 3mg 19%
Potassium 854mg 18%
*The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.
Nutrition information is calculated using an ingredient database and should be considered an estimate. In cases where multiple ingredient alternatives are given, the first listed is calculated for nutrition. Garnishes and optional ingredients are not included.