Preheat the oven to 350℉ and spray a 9x13-inch casserole dish with nonstick cooking spray. Set aside.
Mix the shredded cheddar cheese, mozzarella cheese, and pepper jack cheese together in a bowl and set aside.
Heat the avocado oil in a large skillet set over low/medium heat. When the oil is fragrant, place 2 corn tortillas in the skillet and heat on both sides until they become pliable, about 1-2 minutes total.
When the tortillas are warm and can be rolled without breaking, wrap them in a clean kitchen towel. Repeat until all tortillas are warm.
Pour 1/2 cup of enchilada sauce to the bottom of the casserole dish and spread it in an even layer.
Assemble the enchiladas: Place one tortilla on a work surface and add 1/2 cup of the shredded cheeses and 1 tablespoon of diced onion to the middle. Roll the tortilla and place it seam-side down in the enchilada sauce at the bottom of the of the casserole dish. Repeat until all tortillas are filled and tucked snugly in the baking dish.
Pour the remaining enchilada sauce over the tortillas and sprinkle with the remaining shredded cheese.
Bake for 30 minutes or until the cheese is bubbling and golden brown.
Remove from the oven and sprinkle with the queso fresco. Enjoy with your favorite enchilada toppings!