Preheat oven to 375 degrees. Place a medium-sized pan over medium heat with 1 tablespoon ghee or olive oil. Saute bell pepper, ham, and onion for 3-5 minutes or until soft. Set vegetable mixture aside.
In a large mixing bowl, combine eggs, milk, salt, and red pepper flakes. Whisk to combine.
Prepare a muffin tin with muffin liners or grease well with ghee or olive oil. Fill each muffin cup with 2 tablespoons of vegetable mixture. Pour whisk eggs over the vegetables, leaving about 1/4″ from the top of the muffin tin.
Place in the oven and bake for 15 minutes. Remove from oven and top with chives and cheddar cheese (optional) if desired. Place back in the oven for 5 minutes, or until center is set and the edges start to brown.
