Heat a large oven-proof skillet over medium high heat. Add bacon and cook until brown and crispy, about 6-8 minutes. Transfer bacon to a paper towel-lined plate. Drain bacon fat from the skillet, leaving 1 TBSP in bottom of pan.
To the skillet, add 3/4 of each diced peppers. Saute over medium heat, stirring occasionally until tender and browned, about 3 to 4 minutes. Season with salt and pepper to taste. Stir in green chilies and continue to cook 2 minutes.
In a large bowl, whisk together eggs, milk, cumin, minced onion and bacon. Add to skillet with vegetables and stir until combined.
Float reserved peppers on top of the egg mixture. Cook, undisturbed, until edges are set, about 2 minutes.Place into the oven and bake until top is set and golden brown, about 14 to 15 minutes. Serve immediately.