Place a rack in the centre of the oven and preheat to 325F. Place a silicone muffin pan inside a water tight pan, such as a 9" x13" glass pan or a roasting pan. Grease the muffin cups, then set aside.
To a blender, add the eggs, cottage cheese, pecorino, salt and pepper. Blend until just fully blended and no visible pieces of cottage cheese remain. Do not over blend.
Divide the peppers and mushrooms, the bacon and the cheddar evenly amongst the muffin cups. Pour in the egg mixture, filling each cup nearly to the top. Bring water to a boil. Place the glass pan with the filled muffin pan into the oven. To make a water bath, carefully pour boiling water into the glass pan (between the glass pan and the silicone muffin pan) until it comes half way up the muffin cups. Bake for 20-25 minutes, or until egg bites are set and a toothpick inserted in the centre comes our clean. Remove the muffin pan from the water bath, and allow the egg bites to cool in the muffin pan for 5 minutes. Pop the egg bites out of the pan and serve warm, or set aside to cool. Egg bites can be refrigerated in a covered container for up to 3 days.