Preheat the oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish.
Warm a skillet over medium heat. Add olive oil and sauté the onion for 3–4 minutes until soft.
Stir in garlic and cook 30 seconds until fragrant.
Add butter to the skillet. Once melted, sprinkle in almond flour and whisk for 30 seconds to make a light roux.
Slowly whisk in chicken broth until smooth. Stir in heavy cream, cumin, chili powder, smoked paprika, and a pinch of salt and pepper.
Simmer 2–3 minutes to thicken slightly.
Turn off the heat. Whisk in Greek yogurt or sour cream until the sauce is silky. Stir in green chiles.
Taste and adjust seasoning.
In a bowl, combine shredded chicken with 1 cup of cheese and 1/2 cup of the warm sauce. Mix until coated but not soggy.
Soften tortillas if needed (10–15 seconds in the microwave under a damp paper towel). Divide the chicken mixture evenly among tortillas.
Roll and place seam-side down in the baking dish.
Pour the remaining sauce over the enchiladas, covering evenly. Sprinkle the remaining 1 cup of cheese on top.
Bake for 18–22 minutes, until the cheese is melted and the edges are bubbling. For a golden top, broil 1–2 minutes at the end, watching closely.
Rest 5 minutes.
Garnish with cilantro and serve with lime wedges if you like.