Cook the quinoa: Rinse 1/3 cup dry quinoa under cold water. Combine with 2/3 cup water and a pinch of salt.
Bring to a simmer, cover, and cook until fluffy, about 15 minutes. Fluff and let cool slightly.
Prep the oven and pan: Heat the oven to 375°F (190°C). Lightly oil a 9x13-inch baking dish.
Spread a thin layer of enchilada sauce across the bottom.
Sauté aromatics: Warm olive oil in a skillet over medium heat. Add the onion and cook until soft, 4–5 minutes. Stir in garlic for 30 seconds until fragrant.
Build the filling: Add cumin, chili powder, smoked paprika, and oregano to the skillet.
Stir for 30 seconds to bloom the spices. Add black beans, corn, and green chiles (if using). Season with salt and pepper.
Remove from heat and stir in the shredded chicken and cooked quinoa.
Adjust moisture: Add 1/4 to 1/3 cup enchilada sauce to the filling if it looks dry. You want it moist but not soupy.
Warm the tortillas: To prevent cracking, wrap tortillas in a damp paper towel and microwave 30–45 seconds. Or lightly toast them in a dry skillet for 15–20 seconds per side.
Assemble: Spoon 1/3 cup of filling onto a tortilla.
Sprinkle with a little cheese. Roll snugly and place seam side down in the prepared baking dish. Repeat with remaining tortillas and filling.
Sauce and cheese: Pour the remaining enchilada sauce evenly over the rolled tortillas.
Top with the rest of the cheese.
Bake: Cover with foil and bake for 15 minutes. Uncover and bake 8–10 minutes more, until the cheese is melted and bubbly and the edges are slightly crisp.
Finish and serve: Let rest for 5 minutes. Top with chopped cilantro.
Serve with lime wedges and a dollop of Greek yogurt or sour cream if you like.