Oven BakedEnchiladasblack beansbutternut squashRed Enchilada Sauce

Butternut Squash Enchiladas

Nutriforks
Nutriforks
·8 min read·Published: Apr 13, 2026
Butternut Squash Enchiladas
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These Butternut Squash Enchiladas are filled with roasted squash, black beans, and cheese. A hearty vegetarian fall dinner that freezes perfectly. Get the recipe!

Fall pairs well with Butternut Squash Enchiladas, Three Bean Tacos, and Black Bean and Quinoa Enchilada Zucchini Boats too.

Why Butternut Squash and Black Beans Make Such a Good Pair

Roasted butternut squash brings a natural sweetness and creamy texture that balances the smoky, earthy black beans in these enchiladas. The combination feels like fall on a plate, especially when you add a little cumin, chili powder, and smoked paprika. I like to roast the squash until the edges are just starting to brown, which concentrates its flavor and keeps it from turning mushy inside the enchiladas.

Reasons to Love These Butternut Squash Enchiladas

  • The roasted squash adds a subtle sweetness that pairs perfectly with the spiced black beans and melted cheese.
  • This is a hearty vegetarian fall dinner that even meat-eaters will ask for seconds.
  • You can assemble the whole dish ahead of time and freeze it for a busy weeknight.

Key Ingredients for Butternut Squash Enchiladas

  • Butternut squash: Look for a squash that feels heavy for its size with firm, unblemished skin. A small squash (about 2 pounds) will give you the 3 cups of cubes you need. Pre-cut cubes from the store work too, just make sure they are fresh and not dried out.
  • Black beans: Canned black beans are convenient. Rinse and drain them well to remove excess sodium and starch. You can also cook dried beans from scratch, but canned keeps this recipe quick.
  • Enchilada sauce: Use your favorite red enchilada sauce, either store-bought or homemade. The sauce adds moisture and tang. If you prefer a milder flavor, look for a mild variety.

Kitchen Tools for Butternut Squash Enchiladas

  • Large baking sheet for roasting the squash
  • Large skillet for cooking the onion and pepper
  • 9×13-inch baking dish (glass or ceramic works well)
  • Microwave or small skillet for warming tortillas

Tips for Working with Butternut Squash and Tortillas

You’ll need 3 cups of cubed butternut squash, which is about the amount from one small squash. If your squash is larger, save the extra for another recipe. To cut a butternut squash safely, first trim off the top and bottom, then peel with a vegetable peeler. Cut it in half lengthwise, scoop out the seeds, and cube the flesh into 1/2-inch pieces.

For the tortillas, warming them is essential. Wrap a stack of corn tortillas in damp paper towels and microwave on high for 30 seconds, then flip the stack and heat another 30 seconds. If you prefer, you can briefly fry each tortilla in hot oil until pliable. Either method prevents tearing when you roll the enchiladas.

If you’re planning to deliver these to a friend, assemble them in a disposable foil pan. Write the baking instructions on the lid so they can finish baking at home.

Tips for Making the Best Butternut Squash Enchiladas

To keep your tortillas from tearing, wrap them in damp paper towels and microwave for 30 seconds, then flip and heat another 30 seconds. You can also briefly fry them in hot oil, which adds a little crispness. Either way, warm tortillas roll much more easily.

When roasting the squash, spread the cubes in a single layer on the baking sheet so they cook evenly. Toss them halfway through if your oven has hot spots. The squash is done when a fork slides in easily but the cubes still hold their shape.

If you’re making these for a friend, assemble them in a disposable foil pan. Write the baking instructions on the lid so they can finish it at home.

Ways to Change Up These Enchiladas

If you want to add meat, stir in shredded cooked chicken or ground beef along with the black beans. For a spicier version, use pepper jack cheese instead of Monterey Jack and add a diced jalapeno to the filling. You can also swap the corn tortillas for flour tortillas, though the texture will be softer and less sturdy. To make these vegan, use a dairy-free cheese alternative and skip the queso fresco garnish.

What to Serve with Butternut Squash Enchiladas

Top each serving with sliced avocado, fresh cilantro, pickled jalapeno slices, and a sprinkle of queso fresco. A dollop of sour cream or crema adds a cool, creamy contrast. For a complete meal, serve the enchiladas with Mexican rice, refried beans, or a simple green salad with lime vinaigrette. The bright, tangy salad helps cut through the richness of the cheese and sauce.

How to Store Leftover Butternut Squash Enchiladas

Store any leftover enchiladas in an airtight container in the refrigerator. They will keep for several days. To reheat, cover and warm in a 350°F oven or microwave until heated through. The enchiladas also freeze well, so you can double the batch and save one for later.

How to Freeze Butternut Squash Enchiladas

These enchiladas freeze beautifully. Assemble the dish completely but do not bake. Cover tightly with foil and freeze for up to 3 months. When you’re ready to bake, thaw the dish overnight in the refrigerator, then bake as directed. You can also bake from frozen, but the baking time will be longer. Check that the center is hot and bubbly before serving.

Best Ways to Reheat Leftover Enchiladas

To reheat individual portions, microwave on high until warmed through. For a larger batch, cover the dish with foil and warm in a 350°F oven until heated evenly. The oven method helps the cheese melt smoothly and keeps the tortillas from getting soggy.

Frequently Asked Questions About Butternut Squash Enchiladas

Can I use frozen butternut squash?

Yes, you can use frozen cubed butternut squash. Thaw it first and pat dry to remove excess moisture, then roast as directed. The roasting time may be slightly shorter since frozen squash is often parcooked.

Can I make these enchiladas ahead of time?

Absolutely. Assemble the enchiladas in the baking dish, cover, and refrigerate for up to 24 hours before baking. You may need to add a few minutes to the baking time if starting from cold.

How do I prevent the tortillas from tearing?

Warming the tortillas is key. Wrap them in damp paper towels and microwave for 30 seconds, flip, and heat another 30 seconds. Alternatively, briefly fry them in hot oil. This makes them pliable and less likely to crack when rolling.

Can I use a different type of cheese?

Yes. Monterey Jack and cheddar are classic, but you can use pepper jack for heat, a Mexican blend, or even crumbled queso fresco mixed into the filling. Avoid very soft cheeses like mozzarella as they can make the filling too wet.

Recipe

Butternut Squash Enchiladas

Butternut Squash Enchiladas

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!

mediumVegetarian

15 min

Prep Time

50 min

Cook Time

1 hr 5 min

Total Time

12

Servings

Dinner

Course

Mexican

Cuisine

338 kcal

Calories

Ingredients

Servings
  • 3 cup cubed butternut squash
  • 1.5 tbsp olive oil, divided
  • Kosher salt and black pepper, to taste
  • 0.5 cup red onion, chopped
  • 1 red pepper, stemmed, seeds removed, and chopped
  • 3 garlic cloves, minced
  • 0.333 cup chopped cilantro
  • 0.5 tsp ground cumin
  • 0.5 tsp chili powder
  • 0.5 tsp smoked paprika
  • 15 oz black beans, rinsed and drained
  • 2 cup red enchilada sauce
  • 12 corn tortillas
  • 2 cup shredded Monterey Jack or cheddar cheese
  • avocado, for garnish
  • jalapeno slices, for garnish
  • cilantro, for garnish
  • queso fresco, for garnish

Instructions

  1. 1

    Preheat the oven to 400 degrees F.

  2. 2

    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.

  3. 3

    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.

  4. 4

    Stir 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.

  5. 5

    Spray a 9x13-inch baking dish with nonstick cooking spray.

  1. 6

    To assemble the enchiladas, spread about ¼ cup of the enchilada sauce onto the bottom of the greased baking dish.

  2. 7

    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 from tearing.

  3. 8

    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.

  4. 9

    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.

  5. 10

    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.

Nutrition (per serving)

338kcal

Calorie breakdown

Protein22%76 kcal
Fat38%132 kcal
Carbohydrates40%138 kcal
How this was calculated — 18 of 18 ingredients matched
cubed butternut squashSquash, winter, butternut, raw324 kcal
olive oilOil, corn, peanut, and olive199 kcal
Kosher salt and black pepperPepper, banana, raw0 kcal
red onionOnions, red, raw53 kcal
red pepperPeppers, sweet, red, raw0 kcal
garlic clovesGarlic, raw4 kcal
chopped cilantroCoriander (cilantro) leaves, raw18 kcal
ground cuminSpices, cumin seed9 kcal
chili powderSpices, chili powder7 kcal
smoked paprikaSpices, paprika7 kcal
black beansBeans, black, mature seeds, raw1450 kcal
red enchilada sauceSauce, enchilada, red, mild, ready to serve144 kcal
corn tortillasTortillas, ready-to-bake or -fry, corn26 kcal
shredded Monterey Jack or cheddar cheeseCheese, caraway1805 kcal
avocadoAvocados, raw, Florida1 kcal
jalapeno slicesPeppers, jalapeno, raw0 kcal
cilantroCoriander (cilantro) leaves, raw0 kcal
queso frescoCheese, fresh, queso fresco3 kcal
Serving size ≈ 196 g · 12 servings

Nutrition information is automatically calculated from USDA FoodData Central, so should only be used as an approximation. Actual values may vary depending on the ingredients, brands, and preparation methods used.

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Keyword: fall, gluten-free, kid-friendly, mexican, Oven Baked, vegetarian

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Tags:fallgluten-freekid-friendlymexicanvegetarian

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Nutriforks

NutriForks is a home-cooking site built around two simple ideas: recipes should actually work, and you should know what’s in them. Every recipe pairs clear, tested instructions with a full nutrition breakdown, so healthy, everyday cooking is genuinely easy.

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