Healthy Vegan Enchilada Casserole
Healthy Vegan Enchilada Casserole! Layers of beans, sweet potatoes, homemade enchilada sauce, dairy-free cheese and tortillas. A must-make!
How amazing does this healthy vegan enchilada casserole look? After making a batch of my homemade enchilada sauce this weekend, I decided to share with you a weeknight inspired recipe. All of the flavor of sweet potato and black bean enchiladas, with half of the work.
Dare I saw I actually prefer this casserole over traditional enchiladas because it’s so easy to assemble. Make the filling, make the sauce, put together and bake! I can throw this together in the morning for easy meal prep for dinner.
We love enchiladas in my house. And by we, I mean my husband and I. My kiddos still pick out the peppers and mostly try to eat the beans, potatoes, tortilla and cheese if they can help it. I’ve made countless versions of vegan enchiladas before and if you like those, then you are going to love these.

Ingredients you’ll need
You likely already have most of these ingredients in your pantry. Here is everything you will need:
- Onion
- Red Bell Pepper
- Canned Diced Green Chiles
- Black Beans & Chili Beans
- Sweet Potatoes
- Homemade (or canned)Â enchilada sauce
- Corn tortillas
- Shredded dairy-free cheese or regular cheese as desired

Vegan Enchilada Casserole Instructions
First, you’ll make the sweet potato and bean filling. Start by heating olive oil in a large skillet and sauté the onion and bell pepper for a few minutes until soft. To keep things easy, I’m using canned green chilies, chili beans in sauce and black beans. Add those to the skillet along with the sweet potatoes and spices.
Once the filling and homemade enchilada sauce is made, this casserole comes together very quickly in a baking dish. I added in a few prep photos so you could see how I layered it. The easiest way to fit the tortillas is to half them and layer them as shown in the prepared casserole dish.
For a less soggy filling, I recommend toasting the tortillas first. The easiest way to do this is using a gas burner, but microwaving tortillas for 10 seconds works as well. Turn on the gas burner and hold the tortillas lightly over the gas for 10-15 seconds until warmed through and softened. You don’t have to do this step at all, but if you have the time then I recommend it.
Cover the casserole with foil to help it steam as it cooks. Tenting the foil will prevent it from sticking to the dairy-free cheddar cheese as it bakes in the oven. Remove the foil after 20 minutes, then bake an additional 10 minutes until cheese is bubbly and casserole is hot.
What toppings should I use?
When I make this enchilada casserole, I love adding a few toppings on top for both taste and appearance. Chopped avocado, cilantro and dairy-free sour cream all work great here.

Can you make this gluten-free?
To make this vegan enchilada casserole gluten-free you’ll want to use corn tortillas and a gluten-free enchilada sauce. If using my homemade enchilada sauce, sub in gluten-free all purpose flour or almond flour to make the roux.
Can I use different vegetables in this casserole?
My rule of thumb for enchiladas is this, if they taste good together then it will probably taste good layered between tortillas and smothered with sauce and cheese.
Sweet potatoes pair perfectly with black beans but you can also use butternut squash, summer squash like zucchini or yellow squash, more peppers or leafy greens like kale.

What vegan cheese is best?
If you’ve ever tried dairy-free cheese, then you know they are not created equal. Some are fine, some are delicious and some are downright disgusting. I’m partial to both Violife and Chao cheese when I eat dairy-free. Pictured here is the just like cheddar shreds from Violife and I highly recommend that brand if you can find it. It melts slightly, has a creamy, cheesy taste and most important of all– doesn’t taste like plastic!
Dairy cheese is also a fine substitute if you’d like. Cheddar, pepper jack or Monterey jack would all work great here.
Nutrition for this Vegan Enchilada Casserole
This casserole is loaded with plant-based protein, fiber and healthy fats. One serving contains roughly 330 calories, 10g of protein, 50g of carbohydrates and 10g of heart-healthy fats.

If you like this Vegan Enchilada Casserole, you’ll love these Enchilada recipes
- Veggie Fajita Enchiladas
- Vegetarian Zucchini Enchiladas
- Sweet Potato and Black Bean Enchiladas
- Spinach and Lentil Enchiladas
- Instant Pot Quinoa Enchiladas
- Enchilada Skillet
- Salsa Verde Enchiladas
- Quinoa Enchilada Casserole
If you try this vegan enchilada casserole, make sure to come back to leave a comment and rate it! Your feedback helps others and seeing you make my recipes makes my day.

Healthy Vegan Enchilada Casserole

Equipment
Ingredients
- 1 tablespoon olive oil
- 1 medium white onion, peeled and diced
- 4 ounce can diced green chilies
- 1 red bell pepper, diced
- 15 ounce can chili beans in sauce
- 15 ounce can pinto or black beans, drained and rinsed
- 1 cup peeled and finely diced sweet potato
- 1/4 cup vegetable broth
- 1 batch Homemade Enchilada Sauce, or 3 cups enchilada sauce
- 12 corn tortillas, halved
- 2 cups shredded non-dairy cheese
- Toppings of choice: chopped fresh cilantro, diced red onion, thinly sliced green onion, avocado
Instructions
- Before you being, preheat oven to 350 degrees F. Meanwhile, lightly grease a 9×13″ pan and set aside.
- First, heat the oil in a large sauce pan over medium heat. Add the onion and pepper and cook for 5-6 minutes, or until softened. Next, stir in the chilies, beans, sweet potatoes and broth and cook until sweet potatoes are just tender, about 8 minutes. And, if the potatoes start to stick, add in more broth if needed.
- Next, add in 2 cups enchilada sauce and stir together to combine.
- Then, pour 1/2 cup of the remaining enchilada sauce into the prepared baking dish and spread until evenly coated. Top with a layer of ~8 tortilla halves (see photo for how to layer). Then, top with 1/3 of the enchilada mixture and 1/3 of the shredded cheese. Repeat with another layer of tortillas, enchilada mixture and cheese. Follow by a final layer of tortillas, enchilada mixture, remaining 1/2 cup of sauce and cheese.
- Lastly, cover the pan with foil, then bake for 20 minutes. Remove foil and bake uncovered for 10 minutes, until bubbly and hot.
- Finally, remove and let cool for at least 5 minutes, then top with desired toppings and serve.