Vegan Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt

Last Updated on September 19, 2025 by Christin Gillespie

This Vegan Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt is a comforting recipe made with healthy ingredients. A grain- & gluten-free meal packed with protein-rich black beans, roasted butternut squash, red enchilada sauce, & homemade cashew queso. Topped with creamy avocado, a zesty jalapeño yogurt sauce, & fresh cilantro for the perfect cozy fall or winter dish that’s both wholesome & delicious!

Hearty, healthy, & with a bit of kick, this Vegan Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt is an ultra-cozy vegan recipe for your fall & winter menu.

While you find any tortillas in this enchilada bake, don’t let that turn you away! It’s still super satisfying, thanks to the wholesome combination of protein-rich black beans & sweet butternut squash. The texture is hearty, without feeling heavy.

Each bite is full of flavor from the red enchilada sauce & the homemade cashew queso that ties everything together. However, the jalapeño yogurt is what takes this bake to the next level. It’s cool, spicy, & a bit tangy.

It’s the perfect cozy creation to enjoy on any evening & one that’s sure to become a favorite! 

Why This Vegan Enchilada Bake Hits the Spot

• Untraditional, Yet Totally Tasty: The hearty combination of black beans & butternut squash means you won’t even miss the tortillas.
• Healthy & Not Heavy: Completely plant-based & dairy-free, so you can enjoy your enchiladas with ease.
• Perfect for Any Occasion: Whether you’re nourishing the family, hosting a weekend gathering, meal prepping for the week, or just craving a comforting weeknight dinner, this bake checks all the boxes.

Ingredients

• Organic Butternut Squash: Naturally sweet & tender, butternut squash adds a hearty, comforting texture to every bite of this enchilada bake. Tip: You can also use honeynut squash for an even sweeter, more flavorful alternative!
• Organic Black Beans: Packed with plant-based protein & full of fiber, beans are a staple for any wholesome vegan meal. 
• Red Enchilada Sauce: Duh?! It wouldn’t be enchiladas without it. I used red enchilada sauce, but feel free to swap with green enchilada sauce if that’s more of your vibe. Either way, please use a high-quality sauce. Siete Foods is one of my favorite brands for clean ingredients & phenomenal taste.
• Organic Cashew Queso: It’s rich, dairy-free, & ties the whole dish together. It embodies the cheesy flavors, without any actual cheese.
• Organic Jalapeño Yogurt: A zesty, tangy drizzle with a bit of a kick that perfectly elevates the bake. 
• Organic Garnishes: Creamy avocado, extra jalapeño slices, & a sprinkle of fresh cilantro are what I love to finish this dish off with, but feel free to top it with your go-to’s!

How to Make

1. Roast the Butternut Squash. Preheat the oven to 425°F (220°C). On a baking sheet, toss the cubed butternut with the oil & seasonings. Transfer to the oven & roast for 20–25 minutes, flipping halfway through.
2. Cashew Queso. Add all of the ingredients to a high-speed blender & blend until totally smooth. If the queso is thicker than you’d like, add more spring water by the tablespoon until it’s the right consistency for you. 
3. Mix the Filling. In a large bowl, combine the black beans, roasted butternut squash, red enchilada sauce, & cashew queso. Stir gently until well combined.
4. Bake. Transfer the mixture to a casserole-safe dish & spread evenly. Bake uncovered at 425°F (220°C) for 15–20 minutes.
5. Jalapeño Yogurt. Add all of the ingredients to a high-speed blender & blend until totally smooth. If the sauce is thicker than you’d like, add more spring water by the tablespoon until it’s the right consistency for you.
6. Serve. Remove from the oven. Top with sliced avocado, extra jalapeño slices, a drizzle of the jalapeño yogurt, & fresh cilantro, if desired. Enjoy!

From Good to Great: Your Enchilada Bake Game Plan

• Organic Red Enchilada Sauce: Feel free to swap with green enchilada sauce if that’s more of your vibe. Either way, please use a high-quality sauce. Siete Foods is one of my favorite brands for clean ingredients & phenomenal taste.
• Organic Coconut Yogurt: Be sure to use a plain flavor as well as a clean brand. Check out this Coconut Yogurt 101 post for tips, brands, & everything you need to know about the dairy-free alternative.
• Soak Cashews: Prior to blending, make sure to soak your organic raw cashews in hot water for about 10 minutes. This softens them up & ensures that your cashew queso turns out ultra-creamy & smooth. No gritty texture on my watch!

Storing & Reheating

This Vegan Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt is perfect for leftovers & meal prep! It stores beautifully & tastes just as delicious the next day!

Storing. Once cooled, transfer leftovers to an airtight glass container & refrigerate for up to 4 days. 

Reheating. To reheat, preheat the oven to 350°F (175°C). Place your portion in an oven-safe dish. Place in the oven for 15–20 minutes, until warmed through. Tip: if it looks a little dry, add a splash of enchilada sauce or a drizzle of water before reheating.

More Healthy Vegan Enchilada Recipes You’ll Love

• Summer Vegetable & Black Bean Green Enchilada Bake
• Enchilada Cauliflower & Black Bean Fajita Bowl with Jalapeño Crema
• Vegan Refried Bean & Jackfruit Enchilada Bake
• Sheet Pan Jackfruit Enchilada Fajita Bowl
• Black Bean & Sweet Potato Quinoa Enchilada Bake

Sharing Is Caring!

If you make this Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt recipe, please leave a review & rating below. I love hearing from you, & it helps others learn more about the blog as well. Be sure to follow along on Pinterest, Instagram, & TikTok for even more healthy content!

Xoxo.

CMG.

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