Vegan Quinoa and Cauliflower Rice Enchilada Casserole with Butternut Squash Crust is a naturally low-carb recipe that is created with healthy ingredients. With protein-rich quinoa, cooked cauliflower rice, bold enchilada sauce, vibrant spinach, cashew queso, and roasted butternut squash rounds to top it off, it won’t have you missing the tortillas, dairy, or meat!

Fiesta Friday is here, and this one-of-a-kind low-carb enchilada casserole creation is one to put on your list immediately. It’s hearty, cozy, and so satisfying, but it fuels you up without weighing you down (no post-dinner piñata feelings allowed here).
It’s gluten-free, grain-free, and made with healthy vegan ingredients, without compromising on taste whatsoever. The filling features fluffy quinoa, cooked cauliflower rice, baby spinach, red enchilada sauce, and my classic cashew queso. However, the real star of the casserole is the butternut squash crust. It’s an unexpected, yet sweet and seasonal, topping that really sets this healthy enchilada recipe apart.
I know that the title is a mouthful, but in the same manner, so is every bite. It’s big on flavor and nutrition!
Your New Favorite Vegan Enchilada Casserole Recipe
- Comfort Food Without the Discomfort: This crave-worthy enchilada casserole is made with clean vegan ingredients, so you can enjoy it in peace.
- Tortilla-Free and Totally Flavorful: The nutrient-rich swap of butternut squash rounds are used in place of tortillas, which makes this quinoa enchilada casserole naturally low-carb.
- A Fall and Winter Go-To: The ultimate seasonal dish to share with loved ones, for cozy nights in, or for easy meal prep throughout the week!

Ingredients for Vegan Quinoa and Cauliflower Rice Enchilada Casserole
- Organic Butternut Squash: Instead of traditional tortillas, this black bean enchilada casserole uses roasted butternut squash rounds for a naturally sweet, low-carb topping. I suggest selecting a long, narrow-neck squash for slicing the rounds.
- Organic Quinoa: A must-add-in for protein, fiber, and extra vitamins for this vegan casserole.
- Organic Cauliflower Rice: The perfect filling to add extra volume, nutrients, and texture without the grains. Frozen cauliflower rice is always stocked up in my freezer!
- Organic Baby Spinach: A sneaky way to stir in some extra green goodness. Trust me, you or your picky eaters won’t even notice it!
- Red Enchilada Sauce: My go-to brand is Siete Foods, as they currently make it with clean ingredients, and it’s big on flavor.
- Organic Cashew Queso: The homemade cashew queso adds that beloved cheesy vibe without any dairy. A must for any enchilada casserole recipe.
- Organic Garnishes: Toppings are a must! I love creamy avocado and fresh cilantro, but please customize with your favorites.

How to Make a Healthy Vegan Enchilada Casserole
- Quinoa. Cook according to the package instructions and set aside.
- Roast the Butternut Squash. Preheat the oven to 425°F (220°C) and line a sheet pan with parchment paper. Toss the thinly sliced butternut squash rounds with the oil and seasonings. Spread them out in an even layer and roast for 15–20 minutes, flipping halfway through.
- Cashew Queso. Add all of the queso ingredients to a high-speed blender and blend until smooth (not gritty pieces in sight). If the queso is thick and challenging to blend, slowly add in some spring water (a tablespoon at a time) to achieve your desired creamy consistency.
- Mix the Filling. To the pot of cooked quinoa, fold in the cauliflower rice, baby spinach, enchilada sauce, and cashew queso. Stir until everything is fully combined.
- Bake. Transfer the filling mixture to an oven-safe casserole dish. Top with the roasted butternut squash rounds. Bake uncovered at 425°F (220°C) for 10–15 minutes, until heated through and bubbling.
- Serve. Once the casserole is baked to perfection, garnish with sliced avocado, lime slices, and fresh cilantro, if desired. Enjoy!

Tips for the Perfect Butternut Squash Enchilada Casserole
- Select the Best Butternut Squash: Choose a long, narrow-neck squash for slicing the rounds.
- Leftover Squash: For any squash pieces that aren’t suitable for the rounds, roast them up and mix them into the filling for extra deliciousness.
- Soak the Cashews: If you don’t have a great blender, soaking the cashews is a step that you don’t want to skip. It ensures that the cashew queso is smooth and creamy, without any gritty texture.
- Red Enchilada Sauce: This can make or break the casserole, so choose with intention. My go-to brand is Siete Foods, as they currently make theirs with clean ingredients, and it’s big on flavor.
Storing and Reheating This Vegan Enchilada Casserole
- Storing: Transfer the leftovers to a glass container and refrigerate for up to 4 days.
- Reheating: To reheat, preheat the oven to 350°F (175°C) and place your serving in an oven-safe dish. Warm for 15 minutes or until heated through, then enjoy with your favorite toppings!

More Healthy Vegan Enchilada Recipes
- Vegan Black Bean & Butternut Squash Enchilada Bake with Jalapeño Yogurt
- Cheesy Vegan Pumpkin Quinoa Enchilada Bake
- Vegan Purple Sweet Potato, Black Bean, & Kale Enchilada Bake with Avocado Crema
- Vegan Black Bean Enchilada Bake with Pumpkin Sour Cream Sauce
If you made this Vegan Quinoa and Cauliflower Rice Enchilada Casserole with Butternut Squash Crust recipe, it would mean so much to me if you would leave a rating and review below. It truly makes my day; it helps others find the blog too! Don’t miss out, and be sure to follow on Pinterest, Instagram, and TikTok for even more healthy content!
Xoxo.
CMG.
Print
Vegan Quinoa and Cauliflower Rice Enchilada Casserole with Butternut Squash Crust
- Prep Time: 15
- Cook Time: 35
- Total Time: 50
- Yield: 4 1x
- Category: Main Dish
- Method: Oven
- Cuisine: Mexican
- Diet: Vegan
Description
Vegan Quinoa and Cauliflower Rice Enchilada Casserole with Butternut Squash Crust is a naturally low-carb recipe that is created with healthy ingredients. With protein-rich quinoa, cooked cauliflower rice, bold enchilada sauce, vibrant spinach, cashew queso, and roasted butternut squash rounds to top it off, it won’t have you missing the tortillas, dairy, or meat!
Ingredients
Always opt for organic ingredients.
QUINOA
- 1 cup dry quinoa
BUTTERNUT SQUASH
- 1 medium butternut squash, peeled & sliced into ¼-inch-thick rounds
- 2 tsp avocado oil
- Sea salt & black pepper, to taste
CASHEW QUESO
- ½ cup spring water, plus more to thin
- ½ cup raw cashews, soaked in hot water for 10 minutes
- 1 tsp chili powder
- ½ tsp smoked paprika
- 2 tbsp nutritional yeast
- 1 tsp garlic powder
- 1 tsp onion powder
- Sea salt & black pepper, to taste
FILLING
- 2 cups cauliflower rice
- 2 cups baby spinach
- 1 cup red enchilada sauce
TOPPINGS
- Avocado(s)
- Lime slices
- Fresh cilantro
Instructions
- Quinoa. Cook the quinoa according to the package instructions.
- Roast the Butternut Squash. Preheat the oven to 425°F (220°C) and line a sheet pan with parchment paper. Toss the thinly sliced butternut squash rounds with the oil and seasonings. Spread them out in an even layer and roast for 15–20 minutes, flipping halfway through.
- Cashew Queso. Add all of the queso ingredients to a high-speed blender and blend until smooth (not gritty pieces in sight). If the queso is thick and challenging to blend, slowly add in some spring water (a tablespoon at a time) to achieve your desired creamy consistency.
- Mix the Filling.To the pot of cooked quinoa, fold in the cauliflower rice, baby spinach, enchilada sauce, and cashew queso. Stir until everything is fully combined.
- Bake. Transfer the filling mixture to an oven-safe casserole dish. Top with the roasted butternut squash rounds. Bake uncovered at 425°F (220°C) for 10–15 minutes, until heated through and bubbling.
- Serve. Once the casserole is baked to perfection, garnish with sliced avocado, lime slices, and fresh cilantro, if desired. Enjoy!
Notes
Select the Best Butternut Squash: Choose a long, narrow-neck squash for slicing the rounds.
Leftover Squash: For any squash pieces that aren’t suitable for the rounds, roast them up and mix them into the filling for extra deliciousness.
Soak the Cashews: If you don’t have a great blender, soaking the cashews is a step that you don’t want to skip. It ensures that the cashew queso is smooth and creamy, without any gritty texture.
Red Enchilada Sauce: This can make or break the casserole, so choose with intention. My go-to brand is Siete Foods, as they currently make theirs with clean ingredients, and it’s big on flavor.
Storing & Reheating: Transfer the leftovers to a glass container and refrigerate for up to 4 days. To reheat, preheat the oven to 350°F (175°C) and place your serving in an oven-safe dish. Warm for 15 minutes or until heated through, then enjoy with your favorite toppings!










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