This zucchini chicken enchilada casserole has all of the enchilada flavors without the grains or dairy! It’s easily made in one dish and is paleo, whole30, keto, and AIP with modifications.

Low Carb Zucchini Chicken Enchilada Casserole (Paleo, AIP, Whole30)

Living in Texas, you would think that I’ve had tons of enchiladas in my day. To be honest, I’ve really only had them a few times. They were always an option, so I took in for granted. That’s a decision that I deeply regret once I went grain, dairy, and nightshade free. I thought there was absolutely no way that I could recreate it… until I decided to give it a shot anyway

Traditionally, enchiladas are made with corn tortillas, lots of nightshades, and tons of cheese. Lots and lots of cheese! It’s not really a vegetable dense meal, nor is it the first thing that comes to mind when you think “healthy”. But… this zucchini enchilada casserole is!

Why I Love This Zucchini Chicken Enchilada Casserole

It’s low carb, paleo, and has AIP modifications

As someone who is still nightshade free and serves the AIP community, this casserole is made with that in mind, first and foremost. The enchilada sauce is nightshade free, and it’s not made with any extra peppers.

Plus, since it’s grain-free and made with zucchini instead of tortillas, it’s low carb and gluten-free friendly.

Veggies first!

This meal is packed with veggies in the enchiladas themselves, and topped with more! Especially if you’re AIP and are making a homemade nightshade free enchilada sauce, you’re upping your veggie factor even more.

Low Carb Zucchini Chicken Enchilada Casserole (Paleo, AIP, Whole30)

My non-paleo husband liked it!

I’ve shared before how much my husband likes cheese. I was iffy about him enjoying this recipe, but he loved it! He didn’t mind that it was dairy and nightshade free. He just appreciated that it was healthy and flavorful.


The Ingredients You’ll Need For This Zucchini Chicken Enchilada Casserole



This summer squash is the star of the show 😉

Cooked shredded chicken

You can use any method to cook and shred the chicken. I often use the instant pot or the slow cooker, but whatever you prefer!

Enchilada sauce

If you’re paleo, whole30, or keto, you can use a sugar-free enchilada sauce like this. However, if you’re AIP or don’t tolerate nightshades, just follow along with the recipe listed!

Cilantro, green onion, avocado, radish, red onion, coconut cream, and apple cider vinegar

These are all of the toppings for the casserole. The coconut cream and ACV actually makes a mock sour cream!

Low Carb Zucchini Chicken Enchilada Casserole (Paleo, AIP, Whole30)


Zucchini Chicken Enchilada Casserole (Paleo, Whole30, AIP, Low Carb)

  • Author: Michelle
  • Prep Time: 20
  • Cook Time: 15
  • Total Time: 35 minutes
  • Yield: 5-6 servings 1x


For the casserole

  • 11.5 cups sugar-free enchilada sauce (like this, or the recipe below for AIP)
  • 34 medium zucchinis
  • 1 lb pre-cooked shredded chicken
  • 1 medium avocado, sliced
  • 34 radishes, sliced
  • 1/2 red onion, diced
  • 2 tbsp cilantro, chopped
  • 2 tbsp green onion, chopped
  • 12 limes, quartered
  • 1/4 cup coconut cream
  • 12 tsp apple cider vinegar

For the AIP/ nightshade free enchilada sauce

  • 2 tbsp avocado oil
  • 1 medium white onion, diced
  • 1 cup nightshade free tomato sauce (like this)
  • 1/2 cup chicken broth
  • 1/4 cup water
  • 2 tsp garlic powder
  • 2 tsp oregano
  • 2 tsp cilantro
  • 23 tsp horseradish powder
  • 1 tsp sea salt


For the casserole

  • Preheat the oven to 400 F and prepare a large, 2×9 casserole dish
  • Slice the ends off the zucchini and use a mandolin slicer or a peeler to slice the zucchini into long, thin, 1/8″ inch strips. Pat them down with a paper towel or clean dish towel to remove excess water. Set them aside.
  • Line the bottom of the casserole dish with about a third of the enchilada sauce. Layer on the zucchini slices vertically (you’ll have about two rows of 5-6 slices). Add about 1/3 cup of shredded chicken and layer on a few spoonfuls of enchilada sauce. Repeat this process for about 4 layers. Finish the final layer as just zucchini, and top with the remainder of the enchilada sauce.
  • Bake in the preheated oven for 15 minutes and remove to cool.
  • Make the “sour cream” by mixing the coconut cream and apple cider vinegar. Adjust sourness to liking.
  • Top the enchilada casserole with the remainder of the ingredients, saving the lime slices for serving.
  • To serve, use a spatula to carefully cut a slice of the enchiladas. Serve with limes and additional toppings to taste.

For the AIP/ nightshade free enchilada sauce

  • Using a medium sauce pot, add the avocado to medium heat.
  • Sautee the chopped onion until translucent.
  • Stir in the remainder of the ingredients (reserving the horseradish) and bring to a simmer. Simmer for 15 minutes until the sauce thickens.
  • Stir in the horseradish, little by little and adjust the spice to taste.
  • Remove from heat and allow to cool. Blend with an immersion blender before using.


All nutritional information are estimations and will vary. Estimations do not include optional ingredients.

  • Category: casserole
  • Method: oven


  • Serving Size: 1 serving
  • Calories: 225
  • Fat: 10.4g
  • Carbohydrates: 9.7g
  • Fiber: 3.2g
  • Protein: 19.2g

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Low Carb Zucchini Chicken Enchilada Casserole (Paleo, AIP, Whole30)