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Preheat oven to 450°F. Grease a 2-quart square baking dish; set aside. Quarter the chile peppers and remove seeds, stems and veins. Immerse chiles in boiling water for 3 minutes; drain and invert onto paper towels to drain well. Place the peppers, cut-sides up, in the prepared baking dish. Top with pepper Jack (or Mexican blend) and cotija cheeses.
In a medium bowl, combine eggs and milk. Add flour, baking powder, cayenne and salt. Beat with a rotary beater until smooth (or place in a food processor or blender; cover and process or blend until smooth). Pour egg mixture over chile peppers and cheeses.
Bake, uncovered, for about 15 minutes or until a knife inserted into the egg mixture comes out clean. Let stand for 5 minutes before serving.