Cheesy Butternut Squash and Black Bean Enchiladas

These Cheesy Butternut Squash and Black Bean Enchiladas are a comforting, flavor-packed vegetarian dinner you will want on repeat. This meatless enchilada recipe is made with naturally sweet butternut squash and fiber rich black beans along with a homemade Enchilada Spice Blend. 

If you’re looking for cozy Fall meals, butternut squash and black bean recipes like these enchiladas are perfect for adding a plant based meal to your weekly dinner menu.

Original Post:  September 2023 | Post Updated:  August 2025

I have been making different variations of enchiladas over the years and always find them comforting. These butternut squash and black bean enchiladas were inspired by the cooler seasons and my love for warm spices with creamy textures. Plus the gooey cheese pull never gets old! 

Ingredients needed

• Avocado oil. Or use extra virgin olive oil or vegetable oil  or your preferred cooking oil. 
• Red onion. Or sub with white or yellow onion.
• Red bell pepper. Green, yellow or orange work too. 
• Fresh garlic.
• Canned black beans. Drained and rinsed.
• Butternut squash- I’m using frozen butternut squash for convenience but fresh works if roasted or steamed first.
• Fresh cilantro.
• Shredded cheese.  Reduced fat Mexican blend or pepper jack cheese, queso fresco, or cheddar.
• Avocado oil spray. You can replace with any kind of cooking spray.
• Corn tortillas. Whole wheat tortillas or small flour tortillas work too.
• Red enchilada sauce- Mild or spicy, store bought or homemade. 
• Spices. Cumin, paprika, oregano, granulated garlic, coriander, salt and cayenne.

How to make Butternut Squash and Black Bean Enchiladas

Step One: Preheat the oven to 350 degrees F. Microwave the butternut squash according to the package and set it aside. Rinse and drain the black beans. 

Step Two: In a large skillet, add the avocado oil. Add in the onion, peppers and garlic. Saute for 3-4 minutes. 

Step Three: Add in the drained beans and saute for a minute then add in the butternut squash along with the spice blend. Gently smash down the butternut squash. Add in a 1/2 cup of the cheese and blend.

Step Four: Spray the casserole dish with the cooking spray. Wrap tortillas with a damp paper towel. Place tortillas on a microwavable dish and microwave for 45-60 seconds or until soft. 

Pro tip: In many traditional Mexican recipes, tortillas are fried in oil to soften them. To keep this dish lighter, I microwave the tortillas instead- it’s a simple swap that helps reduce the overall fat and calories. If you’d like, you can add a thin layer of enchilada sauce to the bottom of the baking dish before adding the rolled tortillas. Then pour the remaining sauce over the top. This step is optional but adds moisture and flavor.

Step Five: Place about 1/3 cup of the filling mix along the center of each tortilla. Gently roll up  and place seam-side down into the prepared baking dish; spoon remaining bean mixture on top. Coat the enchiladas with the sauce by pouring evenly throughout. Sprinkle the remaining cheese. (If you have leftover mixture, you can add it on top.)

Step Six: Bake uncovered for about 25-30 minutes or until the cheese is nicely melted and bubbling. Serve hot with optional garnishes like sour cream, greek yogurt ( a sour cream replacement) , 4 Ingredient Guacamole, Avocado Cottage Cheese Dip, green onion, salsa or chopped cilantro.

Storing and reheating

Store any remaining leftovers in an airtight container or cover the baking dish with aluminum foil or plastic wrap. Freeze unbaked enchiladas for up to 2 months. 

What to serve with Butternut Squash and Black Bean Enchiladas

• Spanish rice or low carb cauliflower rice.
• Tortilla chips.
• Mexican street corn. 
• Black olives, sour cream, guacamole, avocado slices or salsa. 
• A simple side salad.

Variations

• To spice it up add green chiles, jalapenos or chipotle.
• Change the protein or add more. Tofu, pinto beans, ground turkey or ground chicken tastes yummy if you are not a vegetarian.
• Add more veggies or swap out the butternut squash for Cumin Sweet Potatoes.

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