Preheat the oven to 375 degrees F (190 degrees C). Lightly coat a deep 9×13-inch baking dish with cooking spray.
Combine eggs, onion, mushrooms, ham, milk, Colby-Jack cheese, and goat cheese in a large bowl. Pour egg mixture into the prepared baking dish. Sprinkle with chopped bacon, Parmesan cheese, salt, and pepper.
Bake in the preheated oven until eggs are set and the edges are golden brown, about 30 minutes. Allow to cool slightly, slice into 8 pieces, and serve.
If freezing, place frittata pieces on a cookie sheet in the freezer until frozen. Transfer to an airtight container and store in the freezer until ready to eat. To reheat, place frozen frittata pieces on a cookie sheet and bake in a 275 degrees F preheated oven (135 degrees C) for 20 minutes.
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