Pre heat the oven to 350-degrees F. Then in a medium-sized bowl add the eggs, thyme, milk, garlic powder and a little salt and pepper. Mix until everything is blended.

In a greased muffin tin, place a layer of chopped ham into 9 of the cups. Then using only 1/2 cup of the cheese, add a cheese over each ham layer. Next add the green pepper over the cheese layer. 

Next take the egg batter and spoon or pour evenly into each of the cups. Lastly top each egg cup with the rest of the 1/4 cup of cheese. 

Bake in the oven for approximately 18 - 20 minutes. The eggs will be very puffed up, let them rest for about 4 - 5 minutes and they'll deflate a bit. 

You may need to loosen the cups from the baking pan by taking a butter knife and sliding it between the edge of the cup and the pan. In most cases the cups will pop out easily and are ready to serve.