I absolutely love enchiladas, but I’ve always found that they’re more trouble to make than they’re worth. All the rolling and careful arranging…and then they fall apart when serving anyway! Instead, I make this enchilada casserole for all of the flavor and none of the fuss.
The other benefit of making this enchilada casserole is that it’s easy to pack full of vegetables! And for those looking to lower their carb intake, you end up eating fewer tortillas than you would in traditional enchiladas. That means more protein and fiber, less empty carbohydrates, but still all the cheesy, saucy enchilada goodness you love!
However, if you make this with my sourdough tortillas with fresh milled flour, you also get all the benefits of fresh milled whole wheat! And if you make your own enchilada sauce, this is truly a guilt-free indulgence!

Can I make this enchilada casserole keto?
This enchilada casserole can easily be made keto-friendly! Here are some swaps you can make:
- Tortillas: Swap the tortillas for zucchini and prepare it like I do in my zucchini lasagna. As long as you cut the zucchini thicker than you think you should, it won’t end up watery. You could also swap them for keto tortillas, though I don’t have experience with those and cannot speak to how well they would work.
- Beans & Corn: If you eat beans and/or corn on keto, that’s great – everyone’s body responds differently to them. If you don’t, feel free to omit them or make substitutions. In place of beans, add more chicken for a boost in protein. In place of corn, add more bell peppers for that pop of sweetness. If you add them right before you assemble the casserole, you’ll even get a bit of a crunch, which is delightful!
- Enchilada Sauce – I recommend making your own enchilada sauce so you can control the ingredients. Many canned enchilada sauces have quite a few non-keto ingredients, from thickeners to sweeteners, not to mention all the other questionable additives. For my enchilada sauce recipe, you can substitute the flour with any keto thickener (i.e. arrowroot powder) – just make sure you follow the package instructions for whatever substitute you’re using.

Can I make this enchilada casserole vegetarian or change the vegetables in the filling?
Yes! The filling can honestly be whatever you want it to be – I’ve changed it up many times without issues (this iteration is just our family’s favorite).
To make it vegetarian, swap the chicken for more beans or for a vegetarian substitute of your choosing. I personally avoid soy products for health reasons, so I cannot speak to how well tofu or other soy-based substitutes work. And while I have not tried it (yet), I think that hard boiled eggs would be delicious in this!
If you’re a meat eater, feel free to swap the chicken for another protein of your choice. Shredded pork shoulder is great here, as is ground beef (you could even sneak in some hidden liver).
In terms of the peppers, feel free to mix that up as well. Use whatever peppers you have on hand. When I’m growing peppers in the garden, I use whatever is ripe instead of exactly what’s in the recipe here (and often a mix of hot and sweet peppers). It always turns out delicious.
I also like to mix up the beans. Sometimes I use black beans and sometimes I use pinto beans. If I have other beans on hand, I might use those as well (or instead). Use whatever beans you like!
Share your substitutions in the comments below – I’d love to hear them!
What are some shortcuts to make this enchilada casserole quick & easy?
You can make as much or as little from scratch as you would like or are able. Here are some ways to save time (or make/do yourself for an even healthier casserole):
- Tortillas: You can buy these or make them yourself. To save time on the day of, I like to make tortillas for a meal earlier in the week, then use the leftovers in this casserole. Stale tortillas are often even better than fresh because they soften to the perfect texture, rather than getting too soft!
- Cheese: Buy pre-shredded cheese or shred it yourself in advance.
- Vegetables: Frozen peppers & onions work well here, and they come already chopped and ready to use! Or you can chop them in advance, if you have more time elsewhere in the week for knocking out some meal prep.
- Chicken: I like to bulk prep my shredded chicken to save a ton of time when making dinner (a hack I learned when I was postpartum with my first). However, you can use rotisserie chicken or other pre-cooked meats (like shredded pork shoulder). You could also start with raw meat and just make sure you fully cook it.
- Beans: Canned beans work here, or you can soak/spout/cook them from dried. If you’re using dried beans, feel free to make them a few days in advance.
- Enchilada sauce: You can buy canned enchilada sauce, but you can also make your own in less than 15 minutes with ingredients you likely already have in your kitchen (and it will taste so much better). Again, this is something you can make in advance so that it’s just as easy as canned to use on the day of.

How do I prevent the tortillas from getting too soft?
It may seem a bit extra, but I layer cheese both above and below the tortillas to create a little buffer from the sauce. I find that this helps prevent soggy tortillas, even with leftovers!
You can also use stale tortillas. Since they’re a bit harder going into the casserole, they are able to soften more before they get soggy. I don’t know which is my favorite use for stale tortillas – quesadillas or this casserole!
Does this casserole make good leftovers?
Yes! I love how the flavors blend overnight, so this is one of my favorite leftovers and they keep for up to 4 days. However, the tortillas do become a bit soggier when reheated in a microwave (less so in an oven or toaster oven). Layering the cheese above and below the tortillas helps, but does not entirely prevent this from happening, especially if you use soft tortillas when you make it. Stale tortillas hold up better.
Unfortunately, I wouldn’t recommend this as a freezer meal. The texture of the veggies and especially the tortillas gets too soft for my taste. However, you can prep all of the components of this and keep them in the freezer for easy assembly!

Ingredients
- 2 tbsp butter – or other healthy fat
- 1 medium onion, chopped
- 3 bell peppers, chopped – or other sweet peppers
- 1 poblano pepper, chopped – optional, but recommended for a mild casserole. Feel free to substitute with jalapeno or other hot pepper for some heat!
- 3 cloves garlic, minced
- 2 lbs shredded chicken thighs – or shredded pork shoulder or other meat.
- 1 lb dried black beans, prepared – or 3 cans of beans. Pinto beans also work well here, as I’m sure most beans would!
- 12oz frozen corn
- 4.5oz can diced green chiles
- 30oz red enchilada sauce, divided – either store-bought or homemade (though homemade really takes this to the next level)
- 12 taco-sized (6″) tortillas – either store-bought or homemade! Stale tortillas work particularly well here.
- 4 cups shredded cheese – I prefer either a Mexican blend, or a combination of cheddar and Monterey Jack or mozzarella

Directions
Step 1: Preheat oven to 350°F. Melt butter in a large skillet over medium heat.
Step 2: Add onion and fresh peppers to the skillet and sauté until soft, about 5 minutes.

Step 3: Add garlic and cook until fragrant, about 1 minute.

Step 4: Add chicken, beans, corn, and diced green chiles to the skillet. Mix and cook until warmed through, about 5 minutes.

Step 5: Set aside 1/2 cup of enchilada sauce. Pour the rest into the skillet and mix it in until evenly combined.

Step 6: Pour half of the filling into an 11×17” casserole dish (or a 9×13”, though you may have leftover filling). Spread 1 cup of cheese over the filling, then layer 6 tortillas over the cheese, and top with another cup of cheese. Add the remaining filling, another cup of cheese, and 6 more tortillas. Finish off with the remaining sauce and cheese.
In short: filling, cheese, tortillas, cheese, filling, cheese, tortillas, sauce, cheese.

Step 7: Bake 30 minutes, until cheese is melted and sauce is bubbling.

Step 8: Rest 5 minutes then serve, garnished with your favorite toppings – sour cream, avocado, salsa, pickled jalapenos, cilantro, or even more cheese!
Equipment
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Healthy Chicken Enchilada Casserole
All of the flavor of enchiladas without the fuss. You’d never know that this delicious enchilada casserole was packed with protein, fiber, and veggies – it tastes too good to be so healthy!
- Total Time: 1 hour
- Yield: 12 servings
Ingredients
- 2 tbsp butter
- 1 medium onion, chopped
- 3 bell peppers, chopped
- 1 poblano pepper, chopped (optional, but recommended for a mild casserole – can sub with jalapeno or other hot pepper for heat)
- 3 cloves garlic, minced
- 2 lbs shredded chicken thighs
- 1 lb dried black beans, prepared (or 3 cans of beans)
- 12oz frozen corn
- 4.5oz can diced green chiles
- 30oz red enchilada sauce, divided – make your own to take this to the next level!
- 12 taco-sized (6”) tortillas – stale is actually preferred here!
- 4 cups shredded cheese – a Mexican blend, or cheddar and Monterey Jack or mozzarella
Instructions
- Preheat oven to 350°F. Melt butter in a large skillet over medium heat.
- Add onion and fresh peppers to the skillet and sauté until soft, about 5 minutes.
- Add garlic and cook until fragrant, about 1 minute.
- Add chicken, beans, corn, and diced green chiles to the skillet. Mix and cook until warmed through, about 5 minutes.
- Set aside 1/2 cup of enchilada sauce. Pour the rest into the skillet and mix it in until evenly combined.
- Pour half of the filling into an 11×17” casserole dish (or a 9×13”, though you may have leftover filling). Spread 1 cup of cheese over the filling, then layer 6 tortillas over the cheese, and top with another cup of cheese. Add the remaining filling, another cup of cheese, and 6 more tortillas. Finish off with the remaining sauce and cheese. In short: filling, cheese, tortillas, cheese, filling, cheese, tortillas, sauce, cheese.
- Bake 30 minutes, until cheese is melted and sauce is bubbling.
- Rest 5 minutes then serve, garnished with your favorite toppings – sour cream, avocado, salsa, pickled jalapenos, cilantro, or even more cheese!
Notes
- Layering cheese above and below the tortillas prevents them from becoming too soft. Stale tortillas also help with this!
- If you use a 9×13″ casserole dish and have leftover filling, save it! It’s amazing with eggs (any way) for breakfast.
Nutrition Facts
Amount Per Serving
Calories: 584 kcal
Fat: 24g
Total Carbohydrates: 63g
Fiber: 11g
Protein: 32g
The nutrition data provided here is for informational only and is only an estimate based on an online nutrition calculator. It cannot be verified or guaranteed, and should not be used in the treatment of medical conditions. It should not be considered a substitute for a professional nutritionist’s advice This data should be interpreted and used at your own risk.








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