Butternut Squash Black Bean Enchiladas
Butternut Squash Black Bean Enchiladas, a tasty plant-based enchilada recipe with a butternut squash, black bean, and poblano pepper filling. Super flavorful and great for meal prep!

Love enchiladas but not sure how to make them plant-based? This vegan enchilada recipe has a black bean and butternut squash filling seasoned with onion, poblano pepper, cumin, oregano, and lime juice. Super flavorful!
👉 Ready to learn how to make enchiladas with butternut squash and black beans? Let’s do it!
🫘 Ingredients
- Butternut squash: The base of the enchilada filling, you’ll need 1 medium butternut squash peeled and cut into cubes
- Black beans: Adds a creamy texture to the filling, you’ll need about 1.5 cups (or one can)
- Onion and pepper: A chopped white onion and poblano pepper add flavor and a kick of heat
- Spices: For a flavor boost we’re adding cumin, oregano, salt and pepper, and lime juice
- Tortillas: Large tortillas are best, about 8 or 10 inches (we used 8). You can use flour or corn, but I’ve had better luck with flour tortillas because they’re softer.
- Enchilada sauce: Either red or green enchilada sauce works, I like to choose a lower sodium option if possible.
- Toppings: A sprinkle of cheese (I used vegan Mexican-style cheese) and sliced avocado
- Recommended tools: 9×13 inch baking dish, large pan with lid, large mixing bowl, immersion blender or food processor

🥣 How to make (step-by-step photos)
1️⃣ Step One: Preheat oven and prep enchilada ingredients
Preheat oven to 400 degrees F (about 200 degrees C).
Then cut the butternut squash, drain the black beans, chop the onion, cut the poblano pepper, and juice the lime to prepare for making the enchilada filling.

2️⃣ Step Two: Cook enchilada filling
Next it’s time to make the filling for the black bean and butternut squash enchiladas.
To do this, bring a large pan to medium-high heat and add 2 teaspoons of the oil.
Then add the cut butternut squash, chopped onion, and cut poblano peppers to the pan and cover with a lid. Cook until the squash is softened and beginning to brown, about 15 minutes.
Then add the black beans, ground cumin, dried oregano, lime juice, and a generous pinch of salt and pepper and mix well to combine, cooking another 2-3 minutes.

3️⃣ Step Three: Blend the enchilada filling
Once the enchilada filling is cooked, remove it from the pan into a large mixing bowl and use an immersion blenders to blend the filling until there are no longer large chunks.
Alternatively, you can also add the mixture to a food processor and pulse until well combined.
👉 Why should you blend the enchilada filling? I have tested this recipe both ways, and if you do not blend the filling ingredients then the enchiladas are very messy to eat and the filling ingredients (the cut pieces of butternut squash, black beans, etc.) fall out of the tortilla. By blending you’re making a solid filling paste that not only makes the final enchilada easier to eat, but also helps consolidate the flavors so it tastes better as well.

4️⃣ Step Four: Fill enchiladas
Once the filling is done, it’s time to fill the enchiladas and prep them for baking.
First, pour about 1/4 of the enchilada sauce to the bottom of a 9×13 baking dish so the enchiladas don’t stick to the bottom when baking.
Then take a tortilla and add about 1/3 cup of the butternut squash and black bean filling in a line in the center of the tortilla.
Then roll the enchilada and place it seam side down in the baking dish. Continue rolling the enchiladas until the baking dish is full (about 8 total).
Pour the remaining enchilada sauce on top, then top with a sprinkle of cheese.

5️⃣ Step Five: Bake enchiladas
Now it’s time to bake the enchiladas!
Do this by covering the enchilada baking dish with foil or an oven-safe baking dish cover and baking in the preheated oven for 15 minutes. Then remove the foil from the baking dish and bake another 5 minutes.

6️⃣ Step Six: Garnish and serve
To serve the enchiladas, remove them to a plate and top with sliced avocados. Then serve, and enjoy!

🧊 How to store
- Refrigerator storage: Store leftover enchiladas in an airtight container in the refrigerator for up to 5 days.
- Freezer storage: To freeze enchiladas, store in an airtight container or freezer-friendly bag for up to two months. To thaw, simply remove enchiladas to the refrigerator up to 24 hours ahead of serving.
- To reheat: Reheat in the microwave for 1-2 minutes, on the stovetop for 3-5 minutes, or place into the oven at 400 degrees F (200 degrees C) for 10 minutes.

🌶 More plant-based enchilada recipes
Want more vegan enchilada recipes? Try Zucchini Enchiladas.

Butternut Squash Black Bean Enchiladas
Ingredients
- 1 medium butternut squash cut into 1/2 inch cubes
- 1 small white onion chopped
- 1 medium poblano pepper chopped
- 1 ½ cups black beans drained (from about 1 can)
- 2 teaspoons oil
- 1 tablespoon ground cumin
- 1 tablespoon dried oregano
- 2 tablespoons lime juice from 1 whole lime
- 1 pinch salt and pepper
- 2 cups enchilada sauce red or green
- 8 8-inch tortillas flour or corn
- ⅓ cup Mexican-style cheese or vegan alternative
- 1 whole avocado sliced
Instructions
- Preheat oven and prep ingredients: Preheat oven to 400 degrees F (about 200 degrees C). Cut the butternut squash, drain the black beans, chop the onion, cut the poblano pepper, and juice the lime.
- Cook enchilada filling: Bring a large pan to medium-high heat and add 2 teaspoons of the oil. Then add the cut butternut squash, chopped onion, and cut poblano peppers to the pan and cover with a lid. Cook until the squash is softened and beginning to brown, about 15 minutes. Then add the black beans, ground cumin, dried oregano, lime juice, and a generous pinch of salt and pepper and mix well to combine, cooking another 2-3 minutes.
- Blend the filling: Once the enchilada filling is cooked, remove it from the pan into a large mixing bowl and use an immersion blenders to blend the filling until there are no longer large chunks. Alternatively, you can also add the mixture to a food processor and pulse until well combined.
- Fill enchiladas: Pour about 1/4 of the enchilada sauce to the bottom of a 9×13 baking dish. Then take a tortilla and add about 1/3 cup of the butternut squash and black bean filling in a line in the center of the tortilla. Then roll the enchilada and place it seam side down in the baking dish. Continue rolling the enchiladas until the baking dish is full (about 8 total). Pour the remaining enchilada sauce on top, then top with a sprinkle of cheese.
- Bake enchiladas: Cover the enchilada baking dish with foil or an oven-safe baking dish cover and bake in the preheated oven for 15 minutes, then remove the foil and bake another 5 minutes.
- Garnish and serve: To serve the enchiladas, remove to a plate and top with sliced avocado.
Notes
- Flour or corn tortillas: I tested this recipe with both flour and corn tortillas, and flour tortillas were much softer and had a better texture. The corn tortillas did not stay folded and fell apart. I suggest flour tortillas and if you need gluten free, there are gluten free flour tortillas.
- Why blend the enchilada filling? If you do not blend the filling ingredients then the enchiladas are very messy to eat and the filling ingredients (the cut pieces of butternut squash, black beans, etc.) fall out of the tortilla. By blending you’re making a solid filling paste that not only makes the final enchilada easier to eat, but also helps consolidate the flavors so it tastes better as well.
- Prep ahead: To reduce final cooking time, prep the filling up to 2-3 days ahead of time. You can also prep the entire dish up to 1 day ahead of time before baking.
- Leftovers and storage: Store leftover enchiladas in an airtight container in the refrigerator for up to 5 days. To freeze enchiladas, store in an airtight container or freezer-friendly bag for up to two months.
- Nutrition notes: Nutrition information is an estimate and is calculated with all ingredients included. This recipe is vegan and there is the option for gluten free.