Quinoa Enchilada Bake

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A delicious sweet potato, black bean, and corn Quinoa Enchilada Bake is a nutrition-loaded casserole the whole family will love. While this dish is vegetarian, you won’t miss the meat in this protein-loaded nutritious dinner!

Pair this quinoa enchilada bake with a simple side dish such as this cucumber salad, this mandarin orange salad, or this Italian salad!

Overhead photo of Quinoa Enchilada Bake.

Years ago I shared this healthy Crockpot Enchilada Quinoa and to this day it’s one of the most loved recipes on my site. Over the years I’ve been asked how to convert it from a slow cooker meal to a casserole and today I’m sharing how to do that. While this recipe isn’t an exact replica of the other dish, it’s quickly become a family favorite.

The other recipe uses ground turkey and for this version, we’re using roasted sweet potatoes. If you or anyone you know is on the fence about a vegetarian meal, THIS is the one to serve! It’s incredibly filling and packed with protein from the quinoa and beans. It’s got so many good-for-you ingredients and my boys scarf it down every time I make it!

Peppers, sweet potatoes and onions with spices being roasted.

So let’s get started! First, let’s talk process. This dish takes a bit of upfront work but comes together so easily!

How to make this cheesy Quinoa Enchilada Bake 

  • Roast the vegetables. Onion, sweet potatoes, and red pepper all get oven roasted in olive oil and spices.
  • Cook the quinoa. While the veggies are roasting, get the quinoa cooking! (Check out my how to cook quinoa guide if you’ve never cooked quinoa before!)
  • Assemble in a casserole dish. This is as simple as combining everything together in a large casserole dish: vegetables, quinoa, beans, corn, enchilada sauce, and cheese.
  • Bake. Stir everything together and bake!
  • Top. Add all your favorites to this Quinoa Enchilada Bake — avocado or guacamole, sour cream, fresh lime, pico, etc!


Quinoa (pronounced KEEN-wah) is a super-healthy grain with significant protein. It cooks quickly, too. The only thing to watch out for is this: Quinoa has a natural coating called saponin which can make it taste bitter. Before cooking it, rinse the quinoa in a fine-mesh strainer for 30 seconds to one minute. Saponin helps protect the quinoa plant from pests (because the bitter taste discourages bugs from eating it), so it’s a good thing, but we don’t want that bitterness in our quinoa dishes.

Process shot of quinoa, vegetables and beans being added to a casserole dish.

Below are a few ways to change up this healthy Mexican quinoa casserole.

Dietary modifications

  • To make Quinoa Enchilada Bake vegan: Simply omit the cheese or use a vegan cheese! Since a lot of flavor does come from the cheese, if you’re leaving it out, make sure you have plenty of toppings!
  • To make this meal dairy free: Omit the cheese and make sure to add plenty of toppings!
  • To make this meal gluten free: Ensure the enchilada sauce you’re using is gluten free, as well as any other canned products.

Variation ideas

  • To make a quinoa enchilada skillet meal: Microwave the sweet potatoes, remove the skin, and chop. Sauté onion and bell pepper in some olive oil in a large skillet and then add in the sweet potato chunks. Add spices, black beans, corn, and cooked quinoa. Add enchilada sauce and cilantro. Stir and heat everything through. Sprinkle with cheese and heat until melted. Serve with your desired toppings!
  • Add meat: Brown ground turkey, chicken, or beef and add it to this meal. Make sure to season the meat you use with salt, pepper, and any additional desired seasonings (such as chili powder, paprika, or cumin). Alternatively, you can serve grilled chicken or steak to the side of Quinoa Enchilada Bake. You could also stir in chopped rotisserie chicken to this casserole before baking.
  • Make it spicier: To increase the heat, add in a finely diced jalapeño. You can also use a hot enchilada sauce and bump up the chili powder!
  • Switch vegetables: We’ve made this with a poblano pepper (roasted, instead of the red pepper). Any pepper will work in this dish, but the red pepper did end up as our favorite! If you would like a replacement for sweet potatoes, you can increase the peppers and onions (3 peppers and 2 onions) in place of the sweet potato.

Process shot: Corn being added and enchilada sauce being poured over top of the casserole.

Our favorite toppings on Quinoa Enchilada Bake 

  • Fresh and ripe sliced avocado (or guacamole)
  • Fresh pico de gallo (or salsa)
  • Lime juice (I serve with a few wedges per plate.)
  • Cilantro (finely chopped and sprinkled on top)
  • Sour cream (Fat-free works great.)
  • Tortilla chips (We like eating this as a dip sometimes!)

Process shot for Quinoa Enchilada Bake: everything mix and assembled and then the finished shot.

More quinoa recipes:

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Quinoa Enchilada Bake

5 from 8 votes
A delicious sweet potato, black bean, and corn Quinoa Enchilada Bake is a nutrition-loaded casserole the whole family will love. While this dish is vegetarian, you won't miss the meat in this protein-loaded nutritious dinner!
Print Recipe

Quinoa Enchilada Bake

5 from 8 votes
A delicious sweet potato, black bean, and corn Quinoa Enchilada Bake is a nutrition-loaded casserole the whole family will love. While this dish is vegetarian, you won't miss the meat in this protein-loaded nutritious dinner!
Course Dinner, Main Course, Vegetarian
Cuisine American, Mexican
Keyword Quinoa Enchilada Bake
Prep Time 30 minutes
Cook Time 30 minutes
Veggie Cook Time 30 minutes
Total Time 1 hour
Servings 4 -6 servings
Calories 567kcal
Author Chelsea


  • 1 and 1/2 pounds (2 medium; 5 cups) sweet potatoes chopped into small bite-sized pieces
  • 1 red pepper chopped
  • 1 small yellow onion thinly sliced
  • 2 tablespoons olive oil
  • 1 teaspoon ground cumin
  • 1/2 teaspoon garlic powder
  • 3 teaspoons chili powder separated
  • 1 cup uncooked white quinoa drained and rinsed
  • 2 cups vegetable stock/broth OR water
  • 2 tablespoons freshly squeezed lime juice
  • 1 can (15 ounces) fire-roasted corn drained
  • 1 can (15 ounces) black beans drained and rinsed
  • 1 can (10 ounces) mild red enchilada sauce (homemade or store-bought - Note 1)
  • 1/4 cup chopped cilantro
  • 1 and 1/2 cups sharp Cheddar cheese divided (Note 2)
  • Toppings: chopped avocado, sour cream, tortilla chips, additional lime and cilantro
  • Fine sea salt and freshly cracked pepper


  • VEGETABLES: Preheat the oven to 425 degrees F. Peel and chop sweet potatoes into small bite-sized pieces. Thinly slice the yellow onion and chop the sweet bell pepper. Put all the veggies on a large (full oven size) sheet pan or two half-sheet pans. Toss with olive oil, cumin, garlic powder, 1 and 1/2 teaspoons chili powder, and salt and pepper. (Add to taste; we add 3/4 teaspoon salt and 1/4 teaspoon pepper.) Place in preheated oven and bake for 15 minutes, flip and bake for another 10-15 minutes. Depending on the size of veggies and the tray you're cooking them on (less space = longer cook time), you may need an additional 5-10 minutes. The potatoes and pepper should be fork tender and onions caramelized and slightly crispy. Remove and set aside to cool. Reduce oven temperature to 350 degrees F.
  • QUINOA: Meanwhile, add quinoa and stock (or broth or water) to a small saucepan. Cook according to package directions and then remove from heat and fluff with a fork. Cover quinoa and set aside. 
  • ASSEMBLE: Grease a 9x13-inch baking dish with cooking spray. Pour the cooked and fluffed quinoa into the baking dish. Add the roasted veggie mix ion top, and add the drained corn, drained and rinsed black beans, enchilada sauce, remaining 1 and 1/2 teaspoon chili powder, cilantro, 1/2 cup shredded cheese, and salt and pepper to taste. (I add another 1/2 teaspoons salt -- add to preference.) Gently stir to combine right in the baking dish. Taste and adjust salt and pepper seasoning to taste. (You can also add any additional chili powder/garlic powder/cumin if desired; we like it just as written!)
  • BAKE: Cover the pan with foil and bake for 20-25 minutes. Remove foil, add remaining 1 cup of cheese and bake an additional 7-10 minutes, or until the cheese is fully melted. Remove from the oven and allow to cool slightly. Garnish with your favorite toppings. Our must-haves: chopped avocado, sour cream, chopped cilantro, and plenty of lime juice! We love this with tortilla chips too (eating it as a dip)!

Recipe Notes

Note 1: You can definitely use a hotter brand of enchilada sauce or make your own to determine the heat. The chili powder does add a bit of additional heat though. Also, not all enchilada sauces are made equal; we used Old El Paso® throughout the testing of this recipe.
Note 2: A Mexican cheese blend or even pepper jack can be used in place of the sharp Cheddar

Nutrition Facts

Calories: 567kcal | Carbohydrates: 69g | Protein: 20g | Fat: 24g | Saturated Fat: 10g | Cholesterol: 44mg | Sodium: 859mg | Potassium: 981mg | Fiber: 10g | Sugar: 11g | Vitamin A: 26183IU | Vitamin C: 46mg | Calcium: 390mg | Iron: 4mg

We do our best to provide accurate nutritional analysis for our recipes. Our nutritional data is calculated using a third-party algorithm and may vary, based on individual cooking styles, measurements, and ingredient sizes. Please use this information for comparison purposes and consult a health professional for nutrition guidance as needed.


I love hearing from you when you've made one of my recipes! Tag me on Instagram at @ChelseasMessyApron or leave me a comment below.




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Recipe Rating


  1. 5 stars
    This recipe is AMAZING. It has everything I love in it! Veggie enchiladas without the yucky, gooey tortilla and instead with healthy quinoa! Also I wanted to point out that adding the enchilada sauce in the assemble section is missing. And I am apparently a slow learner because I go over the list and have forgotten to add it twice. So please add it in if only for me lol

    1. Ahh I’m soo glad you enjoyed this! And thank you sooo much for catching that mistake! It’s fixed. Thanks for your comment! 🙂

  2. 5 stars
    I made half with the sauce and half without (catering to family wishes) and I actually enjoyed it better without. Roasting the veggies was so worth the extra time and mess. Thanks for the great recipe, will be added to my regular rotation!

  3. To be honest…I wasn’t that excited to make this dinner. BUT OH MY GOSH!!! It is sooooo good!!!! My kids truly ate it up! I added ground turkey because—let’s be honest, we aren’t vegan and I wanted some kind of meat. But we couldn’t even taste it. Next time I’ll leave the meat out. This recipe is so flavorFULL! And the sweet potatoes aren’t that noticeable. I had to tell my husband that they were in it! 2 thumbs up for me and my family!

  4. I’m wondering if this can be made ahead, frozen, and thawed and reheated? And if so, what that would look like. Would the roasted veggies get mushy if frozen??? I haven’t cooked much with quinoa…
    Thank you

    1. 5 stars
      This recipe freezes exceptionally well and is so yummy. I have successfully frozen it and enjoyed even more when reheated. 😊

  5. 5 stars
    This recipe is a keeper. My kids weren’t crazy about the sweet potatoes, so I will try subbing white potatoes next time. Still way healthier than frozen pizza, right?? For the adults I used Daiya vegan cheddar shreds. Everyone ate a couple of servings, so that is a win.

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