Chipotle Sweet Potato Enchiladas – Sweet Potato Soul

Absolutely delicious Sweet Potato Enchiladas, filled with a smoky chipotle and veggie-pinto bean filling, then smothered in a creamy sweet potato “cheese” sauce. A comforting and hearty plant-based entrée everyone will love—perfect for Cinco de Mayo, Sunday Supper, and Taco Tuesday.

This recipe was originally published on May 24, 2016. It was updated with new recipe information and photos on August 31, 2025.

Enchiladas are one of those tried-and-true, can’t-go-wrong-with-them meals. Wondering what to make for Sunday supper? Enchiladas. Girls’ night? Enchiladas. Need some comfort food after a long and stressful day? Enchiladas. Want to treat yourself? Always enchiladas!

These sweet potato enchiladas are one of my favorite plant-based spins on the dish (the other: green chile enchiladas!). Packed with pinto beans, spinach, corn, and smoky chipotle peppers, then topped with a rich, lightly earthy, and creamy sweet potato “cheese” sauce, they are hearty, comforting, and completely vegan.

No matter the situation, this recipe delivers delicious satisfaction! While there are a few steps involved, each one is beginner-friendly and—most importantly, worth it. This is the kind of recipe you’ll want to keep on hand for both entertaining and everyday comfort food cravings.

For more tasty sweet potato-Mexican fusion recipes, try my Sweet Potato Breakfast Burritos and Sweet Potato Tortilla Soup.

Ingredients

Here’s what you’ll want to grab to make this veggie enchiladas recipe:

Aromatics: We’re talking red onion and fresh garlic. Use bottled minced garlic if needed, but use fresh for the best flavor.

Spices: Ground cumin, chili powder, onion powder, garlic powder, and sea salt.

Oil: Choose a neutral oil—like grapeseed, canola, avocado oil, or vegan butter.

Pinto Beans: For hearty texture and plant protein! Make them homemade or use canned beans (drained well). Looking for a swap? Try black beans, cranberry beans, or chickpeas.

Canned Chipotle Peppers: These are ripe red jalapeños that have been smoked, lending the dish a delightful smoky heat. Reserve (don’t rinse) the adobo sauce that the chipotles are packed in—it contains loads of flavor. Skip this ingredient if you don’t want mildly spicy enchiladas.

Vegetables: Corn and spinach add sweet, earthy flavor, texture, and extra nutrition.

Steamed Sweet Potato: Adds a sweet silkiness to the sauce, coating each bite. For deeper caramelized flavor, use baked sweet potato puree.

Nutritional Yeast: Adds savory, cheesy flavor and a boost of nutrition to the sweet potato sauce. You will need one cup. For the best flavor, use yeast with a good expiration date.

Non-Dairy Milk: Choose an unsweetened milk, such as soy (my preference), oat, or almond.

Arrowroot Powder: Thickens the sauce, making it spreadable. Don’t have it? Swap cornstarch.

Corn Tortillas: Essential for filling and rolling. You can use wheat tortillas, or grain-free tortillas if you prefer.

Flavor Boosters: Tomato paste enhances the veggie filling, while smooth Dijon adds peppery notes and apple cider brings tang to the “cheese” sauce.

How to Make Sweet Potato Enchiladas

First, we’ll prepare the flavorful filling. From there, we’ll quickly make the cheesy sweet potato sauce. To finish, we’ll assemble everything and bake until the enchiladas are hot, bubbly, and perfect!

Make the Veggie and Chipotle Enchilada Filling

Sautè Aromatics. Heat 2 tablespoons of oil in a skillet over medium-high heat. Add the onions and garlic to the skillet, and sauté for 5-6 minutes until tender. Add the cumin and chili powder and stir well to toast the spices for about 30 seconds.

Add Veggies. Stir in the corn, drained pinto beans, tomato paste, chipotle peppers, and spinach until well combined. Bring the mixture to a simmer and cook for 8-10 minutes or until the kale is tender. Remove the pan from the heat and set aside.

Simmer the Sweet Potato Enchilada Sauce

Prepare. Mix the arrowroot in a small bowl with ⅓ cup of the milk until smooth. Set aside.

Cook. To a saucepan add the remaining 2/3 cup of milk, mustard, onion powder, garlic powder, vinegar, nutritional yeast, and salt. Whisk well to combine. Bring to a simmer for one minute. Reduce the heat to low, and whisk in the arrowroot mixture until well combined. Cook, whisking frequently, for about 3 minutes until the sauce has thickened.

overhead cheese sauce ingredients in pot

Blend. Carefully transfer the sauce to a blender and add the steamed, peeled sweet potato. Top the blender with the lid, remove the vent, cover it with a clean towel, and blend the sauce until smooth. If desired, add an extra chipotle pepper or two for a more smoky, spicy sauce.

sweet potato and cheese sauce in blender

Assemble the Enchiladas and Bake

Fill Enchiladas. Preheat the oven to 375°F and grease an 8×13-inch baking dish or cast-iron skillet with non-stick cooking spray or oil. Fill each tortilla with 1/2 cup of the enchilada filling, roll them up, and place them seam-side down in the baking dish.

Bake. Cover the enchiladas with the creamy sweet potato cheese sauce. Bake the enchiladas uncovered for 20 minutes or until heated through and bubbling around the edges.

Serve. Sprinkle the veggie enchiladas with chopped cilantro and serve hot!

Jenné’s Recipe Tips

Blend Carefully: If not properly vented, the hot ingredients can create pressure, causing the lid to blow off. To prevent dangerous and messy splatters, remove the lid’s vent and cover it with a dish towel before blending.
Don’t Overstuff: About 3/4-1 cup is all you need to fill each enchilada. Overfilling can make the enchiladas hard to roll, while inconsistently filling them can prevent even baking. However, the amount of filling will depend on the size of your tortillas.
Roll and Place the Enchiladas Seam-Side Down: This seals the enchiladas, preventing the fillings from seeping out as they bake.
Add Cilantro After Baking: Garnish with fresh herbs (and other toppings of choice, such as avocado, vegan sour cream, pickled onions, or lime) to keep the flavors bright and fresh.

Recipe Variations

One of the many things I love about this veggie enchilada recipe is its versatility—it’s easy to adapt to the occasion, your flavor preferences, and what you have on hand.

Extra Spicy: Blend chipotles into the sweet potato sauce for an extra layer of smoky heat.
Squash: Use roasted butternut squash instead of sweet potato for a cozy autumn variation.
Swap the Peppers: For less heat, try roasted poblano peppers in place of the chipotles in adobo.
Switch up the Beans: Try black beans, kidney beans, or even chickpeas for extra texture and heartiness.
Vary the Veggies: Chopped bell peppers, kale, chopped tomatoes, zucchini or yellow squash, and green beans are all delicious options.
Add Tofu: Chop a block of extra-firm (or a pressed block of firm) tofu into 1/2-inch cubes and sauté it with the onions and garlic for extra plant-based protein. You could even fill them with my tofu sofritas instead of the regular filling.

Storage Directions

Refrigerating: Leftover sweet potato enchiladas keep covered in an airtight container in the fridge for up to 5 days.
Freezing: Once cooled to room temperature, transfer the enchiladas to a freezer-safe container and freeze for up to 3 months. Defrost the enchiladas overnight in the refrigerator before reheating.
Reheating: Warm individual servings of enchiladas in the microwave on gentle heat for 1-2 minutes. For multiple servings, place enchiladas in a covered baking dish and reheat in a 350°F oven for 15–20 minutes, adding extra time if needed, until heated through.

Frequently Asked Questions

Can I make the enchiladas ahead of time?

Certainly! Assemble the sweet potato enchilada casserole, cover it tightly with plastic wrap or aluminum foil, and refrigerate for up to 24 hours. Reheat as directed, adding 5-10 minutes of baking time if starting from cold.

How do I prevent the corn tortillas from cracking?

The secret to preventing corn tortillas from cracking is gently warming them in a skillet for 20-30 seconds or in the microwave on low heat before filling and rolling. Wrap them between layers of a cotton kitchen towel or damp paper towels to keep them warm and soft as you fill them.

Can I use canned sweet potato?

Yes—although I prefer fresh steamed sweet potato for flavor and freshness, canned purée can work in a pinch. Just be sure to use 100% pure sweet potato.

More Vegan Mexican-Inspired Recipes

Veggie and Chipotle Enchilada Filling

Sweet Potato Cheese Sauce

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Veggie and Chipotle Enchilada Filling

Heat the oil in a skillet over medium-high heat.
Add the onions and garlic to the skillet, and sauté for 5 minutes until tender.
Add the cumin and chili powder and stir well to toast the spices for about 30 seconds.
Stir in the corn, drained pinto beans, tomato paste, chipotle peppers, spinach, and salt until well combined. Add 1/4 cup of water to deglaze the pan.
Bring the mixture to a simmer and cook for 5-8 minutes or until the spinach is tender. Remove the pan from the heat and set aside.

Sweet Potato Enchilada Sauce

Mix the arrowroot in a small bowl with ⅓ cup of the milk until smooth. Set aside.
To a saucepan add the remaining 2/3 cup of milk, mustard, onion powder, garlic powder, vinegar, nutritional yeast, and salt. Whisk well to combine.
Bring to a simmer for 1 minute. Reduce the heat to low, and whisk in the arrowroot mixture until well combined. Cook, whisking frequently, for about 3 minutes until the sauce has thickened.
Carefully transfer the sauce to a blender and add the steamed, peeled sweet potato. Top the blender with the lid, remove the vent, cover it with a clean towel, and blend the sauce until smooth. If desired, add an extra chipotle pepper or two for a smoky, spicy sauce.

Assemble and Bake

Preheat the oven to 375°F and grease an 8×13-inch baking dish or cast-iron skillet with non-stick cooking spray or oil.
Fill each tortilla with 3/4-1 cup of the enchilada filling, roll them up, and place them seam-side down in the baking dish.
Cover the enchiladas with the creamy sweet potato cheese sauce. Bake the enchiladas uncovered for 20 minutes or until heated through and bubbling around the edges.
Sprinkle the enchiladas with chopped cilantro and serve hot with quick pickled onions.

Storage Directions

Refrigerating: Leftover sweet potato enchiladas keep covered in an airtight container in the fridge for up to 5 days.
Freezing: Once cooled to room temperature, transfer the enchiladas to a freezer-safe container and freeze for up to 3 months. Defrost the enchiladas overnight in the refrigerator before reheating.
Reheating: Warm individual servings of enchiladas in the microwave on gentle heat for 1-2 minutes. For multiple servings, place enchiladas in a covered baking dish and reheat in a 350°F oven for 15–20 minutes, adding extra time if needed, until heated through.

Recipe Pro-Tips

Blend Carefully: If not properly vented, the hot ingredients can create pressure, causing the lid to blow off. To prevent dangerous and messy splatters, remove the lid’s vent and cover it with a dish towel before blending.
Don’t Overstuff: About 1/2 cup is all you need to fill each enchilada. Overfilling can make the enchiladas hard to roll, while inconsistently filling them can prevent even baking.
Roll and Place the Enchiladas Seam-Side Down: This seals the enchiladas, preventing the fillings from seeping out as they bake.
Add Cilantro After Baking: Garnish with fresh herbs (and other toppings of choice, such as avocado, vegan sour cream, pickled onions, or lime) to keep the flavors bright and fresh.