Easy Butternut Squash Enchiladas

These easy vegan butternut squash enchiladas are slightly sweet, savory, herby, and perfect for enjoying on meat-free Mondays (or any day of the week!) Simple to prepare, low-effort, budget-friendly, and they freeze and reheat well!

Comforting, Crowd-Pleasing Vegan Butternut Squash Enchiladas

Vegan tacos, burritos, and enchiladas always make for a worthy meat-free meal the entire family will adore - these vegan butternut squash enchiladas are no different. Thanks to the squash, these comforting vegan enchiladas are perfect for fall. However, they can be enjoyed year-round for a hearty, flavorful, low-budget, pantry-friendly, and minimal-fuss vegan/vegetarian meal!

These healthy vegan enchiladas combine the flavors of slightly sweet butternut squash with savory cumin and coriander seasoning and vibrant red onion and cilantro filling, all wrapped inside a flavorful corn tortilla. That’s then topped off with spicy and flavorful green enchilada sauce, optional vegan cheese, and the toppings of your choosing.

The result is a hearty and comforting dish that’s tender in the middle, lightly crisp on the edges, and requires minimal ingredients while packing in plenty of flavor. Of course, you can also adapt the recipe to your liking with several ingredient substitutions and add-ins to fit your needs.

There are several ways to reduce prep time and effort for this recipe, too; using canned enchilada sauce, pre-cut butternut squash and/or onion, etc. All in the name of getting these delicious plant-based enchiladas on your plate as quickly as possible.

Best of all, these healthy vegan enchiladas are meal preppable, freezer-friendly, and reheat well—for a delicious last-minute meal any day of the week!

The Ingredients

All you need are 10 simple, inexpensive, plant-based, and primarily pantry-friendly ingredients to prepare vegan butternut squash enchiladas.

ingredients for Easy Butternut Squash Enchiladas measured out against white background

Corn tortillas: I prefer to use 8-inch corn tortillas (naturally gluten-free and sturdier than wheat ones). However, use flour tortillas if preferred.
Butternut squash: Use pre-cooked butternut squash cubes or frozen butternut squash cubes (thawed). Alternatively, you could make sweet potato burritos or use pumpkin cubes instead.

Alternatively, you can use other squash varieties, pumpkin, or even make vegan sweet potato enchiladas.

Oil: Use any neutral cooking oil, like vegetable, canola, grapeseed, avocado, etc.
Seasonings: Cumin, coriander, salt, and black pepper.
Green enchilada sauce: You can use homemade or store-bought enchilada sauce. Red enchilada sauce with this butternut vegetarian enchilada filling will taste just as delicious.
Vegan cheese: (optional) Use either shredded vegan cheese or a vegan cheese sauce to spread over these easy vegan enchiladas.
Red onion: Yellow onion works in its place.
Cilantro: Optional — flat-leaf parsley or green onions would also work.
Toppings: I love to use a combination of finely chopped red onion, cilantro, radish, hot sauce, and lime wedges.

What Else Could I add to the Plant Based Enchiladas?

Black beans: For a heartier, more protein-dense meal, make butternut squash black bean enchiladas (using low-sodium canned or home-cooked beans).
Refried beans: To use in place of a sauce over the vegan enchiladas.
For spice: Use a seeded, diced jalapeño or poblano pepper (adjust the amount to taste) or cayenne/chili powder in the seasoning.
Garlic: Either minced or garlic powder to add to the seasoning.
Pumpkin seeds: To sprinkle over the vegan butternut squash enchiladas for crunch, protein, and heart-healthy fats.
Bell pepper: I usually use either red pepper or green pepper. Cut it into cubed pieces to roast along with the butternut squash for the filling.
Corn: Fresh, frozen (thawed), or canned. To add to the vegetarian enchilada filling for more sweetness.
Spinach/kale: Pre-cooked to remove excess liquid. To add extra nutrients to the plant-based enchiladas.

How to Make Butternut Squash Enchiladas?

1) First, preheat the oven to 400F/205C and prepare the vegetables by peeling, de-seeding, and chopping the butternut squash into bite-sized cubes (about ½-inch in size). Also, finely chop the onion and cilantro.

How To Chop Butternut Squash?

First, slice off both ends of the squash. Then use a vegetable peeler to remove the skin. Slice it in half length-wise, and use a spoon to scoop out the membrane/seedy part. Then make slices every ½-inch across the squash halves and chop them down into ½-inch cubes.

2) Then, transfer the butternut squash pieces, oil, and spices to a bowl and toss everything until well coated. Spread the seasoned squash on a parchment-lined baking sheet and roast until lightly caramelized outside and tender in the middle (around 30 minutes). Then, remove the tray from the oven and set it aside.

butternut squash and spice in a clear bowl against a white background

3) To assemble the butternut squash enchiladas, spread a few tablespoons (enough to coat the bottom of the dish) of the green enchilada sauce across the bottom of an 8x8-inch baking dish.

process shot of adding sauce to baking pan

process shot of spreading sauce on bottom of baking tray

4) Then, divide the butternut squash between the tortillas, topping them each with a teaspoon of enchilada sauce, some red onion, and some chopped cilantro.

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process shot of adding filling to tortilla

To make them easier to roll, first, heat the tortillas (in a stack) for about 30-50 seconds in the microwave.

5) After assembling, roll the enchiladas up and place them in the baking dish seam-side down. Pour the rest of the enchilada sauce over the top, smoothing it with the back of a spoon. Sprinkle over the vegan cheese now, if using, then bake the vegan enchiladas for 20 minutes.

five enchiladas pre-cooked in a baking dish

process shot of adding sauce to enchiladas in baking tray

6) Finally, remove them from the oven and allow them to rest for 5-10 minutes before serving. Enjoy the healthy vegan butternut squash enchiladas with your favorite toppings. I love adding some extra freshly chopped onion, cilantro, and radish, with a lime wedge and hot sauce on the side.

FAQs

Are butternut squash enchiladas healthy?

Although these vegan enchiladas contain minimal ingredients, the butternut squash provides fiber, antioxidants, and several vitamins and minerals. The recipe is also low in fat. You can then tweak it to fit other macro goals (i.e., black beans for protein).

How to avoid soggy enchiladas?

That shouldn’t be an issue with this butternut squash veggie enchilada recipe. However, as a general rule, to avoid soggy enchiladas, fry the tortillas in a little oil for just 10-15 seconds per side before filling and assembling them. The oil helps to create a barrier layer against the sauce.

Can I cook the butternut squash in a skillet?

Cut it into small ½-inch pieces and add 1-2tbsp of oil to the skillet. Then cook the squash over medium heat, stirring occasionally, until tender in the middle and lightly browned outside (this takes 10-15 minutes).

How to use leftover butternut squash filling?

My favorite way is to use it as a topping for a burrito-style rice bowl, with other veggies (corn, beans, lettuce, guacamole), plus salsa and vegan sour cream. Of course, it would also work in tacos and burritos.

What other enchilada toppings could I use?

Avocado slices, guacamole, jalapeño slices (fresh or pickled), vegan cheese sauce, vegan sour cream, salsa, fresh greens like arugula or baby spinach, etc. are all toppings you could enjoy over these healthy vegan enchiladas.

Top Recipe Tips and Notes

For less prep: Use pre-chopped butternut squash and/or onion.
Seam side always down: To ensure the baking enchiladas won’t unravel.
To make the squash easier to cut: Pierce it a few times with a knife, then microwave it for 2-3 minutes before chopping. This will help to slightly soften the flesh for your knife.
For even sauce distribution: Lightly fry the tortillas in oil to create a ‘barrier’ layer, then dip each of the tortillas in the green enchilada sauce before filling and rolling them. Then add any remaining sauce to the top of the dish before baking.
To reduce harsh raw onion flavor: Soak it in ice water for 10-15 minutes.

Storage Instructions

Make ahead: You can store pre-cut butternut squash OR pre-cook the butternut squash filling and store it in an airtight container in the fridge for 2-3 days (it’ll be fine to eat for up to 4 days). Then, assemble and bake as needed.

Fridge: While these baked enchiladas will become softer/soggier over time, the leftovers last 3-4 days in the fridge to reheat (or enjoy cold).

Reheat: Reheat an individual portion in the microwave for a minute or two, or cook them for 10-15 minutes in the oven at 350F/180C.

Can you freeze enchiladas?

I recommend freezing any assembled, unbaked, butternut squash enchiladas individually wrapped in plastic wrap and then placed in a large Ziplock/Stasher bag for up to 3 months (though you can also freeze the entire dish of assembled un-baked enchiladas). You can then thaw and cook them with the sauce or cook them from frozen. Adding extra time as needed.

Alternatively, to avoid the risk of soggier vegan enchiladas, freeze just the filling, ready to assemble enchiladas, burritos, and tacos, as needed.

Serving Recommendations

If I want a light meal, the baked enchiladas are enough when eaten alone or alongside a simple side salad/slaw. However, my favorite way of enjoying this veggie enchilada recipe is with a side of Mexican rice, cilantro lime rice, or low-carb cauliflower rice.

If I want more heart-healthy fats, I’ll enjoy it topped with a few slices of avocado (or some guacamole). Enjoy these healthy vegan enchiladas with some black beans or refried beans for added protein.

More Healthy Vegan Mains

If you try this easy, healthy, vegan butternut squash enchiladas recipe, I’d love to know what you think in the comments below. I’d also really appreciate a recipe card rating!

Photos by Alfonso Revilla