Preheat the oven to 350°F and coat a 9x13 baking dish with cooking spray.
For Using Whole Chiles: Stuff each chile pepper with a stick of cheese or a generous handful of shredded cheese, placing more on top of each pepper. Put the peppers in the pan, evenly spaced. Only use half of your cheese, you'll need the rest for topping. For Using Diced Green Chiles: Evenly spread the chiles in a baking dish. Top with half of the shredded pepper jack cheese and half of the colby jack cheese. Set it aside while you get the egg mixture ready.
In a separate medium mixing bowl whisk together the eggs, milk, salt, and dry powdered mustard until the clumps are gone (some may remain). Spoon out 1/4 cup of eggs mixture to a small bowl and whisk with the flour, making a paste. Whisk it back into the main egg mixture.
Pour the egg mixture over the chiles and cheese.
Bake, uncovered, for 40 minutes. Add the remaining cheese to the top of the casserole and return to the oven for an additional 5 minutes or until the center has set and the cheese has melted.
Remove and allow to sit for 5 minutes before serving.
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Notes
If you prefer to use cream of tarter to fluff up the eggs instead of flour, use 1 teaspoon.Flour can be omitted, if you are looking for gluten-free. This recipe has been modified to use chopped green chiles. If you are used to the old recipe, you can still use whole chiles stuffed with sticks of cheese.