This Zucchini Chicken Enchilada bake is loaded with healthy protein and vegetables and makes a tasty, gorgeous dinner! The AIP-friendly enchilada sauce is made without any nightshades and it gives the chicken stuffing so much flavor.

This recipe is also suitable for the paleo, SIBO, and candida diets. It is also fairly low in carbs and much lighter than traditional enchilada casseroles.

AIP enchilada sauce Enchilada sauce in a medium skillet with wooden spoon stirring

The star of this recipe is the flavorful healthy AIP enchilada sauce made without any gut-irritating tomatoes or peppers. Instead of nightshades, the sauce has a base of carrots and beets and is seasoned with onion, fresh garlic, and dried oregano, and spiced with fresh ginger. I also add fresh lime juice and fresh cilantro to the sauce to give it a Mexican-inspired flavor. 

Not only is this sauce perfect for the AIP diet, but it is loaded with nutrients. Carrots are a great source of fiber, beta carotene, vitamin K1, and potassium. Beets are also high in fiber, and contain a lot of folate and manganese. Onions, garlic, and ginger are loaded with healthy antioxidants. 

This nightshade-free enchilada sauce is used to flavor the chicken filling for the enchiladas and is brushed on top of the zucchini roll ups before baking. Enchilada Sauce on top of rolled zucchini atop a wooden cutting board

The recipe below makes extra sauce – enough to make a double batch of the zucchini chicken rollups, or to use in another recipe in place of tomato sauce (try it with zucchini zoodles!). The leftover sauce will last in the fridge for up to 1 week when stored in a closed jar.

The sauce can be prepared in advance, and once you have the sauce ready, the zucchini enchilada rollups can be put together in just a few minutes!

Zucchini chicken rollups

Thinly sliced zucchini is used instead of tortillas as the base for these chicken enchiladas. I use a vegetable peeler to slice the zucchini lengthwise. You can also use a mandoline slicer on its thinnest setting. You want the zucchini slices thin enough that they roll up easily without snapping or breaking. 

Zucchini makes a great low-carb substitute for tortillas and it is very healthy! It is low in calories but high in vitamins A, C, K, manganese, and folate. It contains fiber to help us with digestion and may help reduce blood sugar levels.

The chicken filling is made by sauteing cooked chicken with chopped onion, nightshade-free enchilada sauce, and a few authentic seasonings: ground coriander, garlic powder, and ground cumin. Zucchini Chicken Enchiladas being layered into a glass baking pan

You can use any cooked chicken that you like for this dish – I like a combination of chicken breast and thigh meat chopped and shredded into small pieces. Dark meat has a little more fat and calories than lean chicken breast, but both are high in protein, vitamin B12, and zinc while being virtually carb-free. This is a great roast chicken recipe to use if you want to make your own roast chicken. 

To make the zucchini chicken rollups, arrange 3-4 thin slices of zucchini so they are overlapping. Add a few tablespoons of the chicken filling with sauce, and roll up the zucchini. Place the zucchini rollups onto a prepared casserole pan that has a few tablespoons of enchilada sauce on the bottom. 

Bake the casserole at 350 degrees Fahrenheit for about 20-30 minutes, or until the zucchini is cooked to your liking. A spatula holding up freshly baked zucchini chicken enchiladas

I like to serve this dish with a dollop of coconut “sour cream,” made by mixing together unsweetened coconut cream with a little lime juice. Colorful garnishes, such as sliced avocado, sliced radishes, and fresh cilantro also go great with these AIP zucchini enchiladas!

This is one of my favorite healthy dinner recipes, and I hope you love it as much as I do!

Other healthy comfort food casseroles to try: 

Zucchini Chicken Enchiladas

Zucchini Chicken Enchiladas

Zucchini Chicken Enchiladas



4 servings

4 servings

Prep Time

20 minutes

Cook Time

30 minutes

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For the zucchini chicken enchiladas:
  • 3 zucchini large
  • 1 1/2 360 cups ml chicken cooked, shredded or chopped
  • 1 onion diced
  • 1 14.787 tbsp ml extra virgin olive oil
  • 1 4.929 tsp ml ground coriander
  • 1/2 2.4645 tsp ml ground cumin
  • 1/2 2.4645 tsp ml garlic powder
For the AIP enchilada sauce:
  • 2 carrot peeled and chopped
  • 2 beets peeled and chopped
  • 1 onion peeled and chopped
  • 3 3 cloves garlic roughly chopped
  • 2 5.08 inches cm ginger peeled and minced
  • 2 480 cups ml chicken broth
  • 1 14.787 tbsp ml dried oregano
  • 1/4 60 cups ml cilantro
  • 1 14.787 tbsp ml lime juice
  • sea salt to taste
  • ground black pepper to taste



Prepare the enchilada sauce:
  1. Heat the olive oil in a large skillet or casserole skillet. Add the chopped onions, carrot, beets, garlic, and ginger, and saute over medium-high heat for about 5 minutes, stirring frequently.
  2. Add the chicken broth and oregano, bring to a boil, then lower the heat and simmer for about 10 minutes, or until the vegetables are fully cooked.
  3. Stir in the lime juice and fresh cilantro, and allow to cool a little.
  4. Use an immersion blender, or transfer the mixture carefully to a blender, and puree until desired texture resembling chunky or smooth tomato sauce. Adjust the seasonings with salt, pepper, and lime juice, if needed. If it is too thick, add a little water. If it is too watery, transfer the mixture back to the pan and simmer for a few minutes, until desired thickness.
  5. Use half the enchilada sauce for the zucchini enchiladas. Store the remaining enchilada sauce in the refrigerator for up to 7 days or freeze it in a freezer-safe container to use for later.
Prepare the zucchini enchiladas:
  1. Preheat the oven to 350 degrees Fahrenheit. Spread about ½ cup of the enchilada sauce on the bottom of an 8x8 inch casserole pan.
  2. Heat the olive oil in a medium skillet. Add the diced onion, and saute for 3-5 minutes, or until the onion softens and starts to brown. Add the diced chicken, 1.5 cups of enchilada sauce, ground coriander, ground cumin, and garlic powder, and continue to cook for 2-3 minutes, stirring to combine. If you like, add a little more sauce to the chicken.
  3. Use a vegetable peeler to thinly slice the zucchini lengthwise. The first few slices will be too narrow to use (you can save them for this zucchini noodle salad for later). You will need 3-4 slices of zucchini per chicken rollup, and you can fit about 6-8 rollups in an 8x8 inch pan.
  4. Arrange 3-4 zucchini slices on a cutting board or flat surface, slightly overlapping, to create a zucchini sheet a few inches wide. Add a few tablespoons of the chicken mixture to one end of the zucchini slices, then roll up. Carefully transfer to the casserole pan, and repeat with the remaining zucchini slices and chicken mixture.
  5. Top each zucchini rollup with a tablespoon of enchilada sauce and sprinkle with fresh cilantro leaves. Bake at 350 degrees Fahrenheit for 20-30 minutes, or until the zucchini is cooked to your liking. Allow to cool for a few minutes, and serve warm, garnishing with your preferred garnishes, such as sliced avocado, fresh cilantro or diced scallion, sliced radish, or a few teaspoons of coconut ‘sour cream.’


Garnishes for serving:

  • Sliced radishes, slice avocado, fresh lime, fresh cilantro or scallion
  • Coconut “sour cream,” made with ¼ cup coconut cream + 1-2 teaspoons lime juice, to taste