Preheat oven to 350°F / 175°C. Grease a silicone muffin tin with oil (see notes).
In a medium pan, sauté onion, green bell peppers and mushrooms together until everything has softened. Cook until the mushrooms have released their own water.
In a large bowl, beat the eggs together. Beat in the milk, garlic (optional), salt and black pepper.
Evenly divide the vegetable mixture into the egg cups. Top each muffin cup with a bit of grated cheddar cheese. Gently pour on the egg mixture into each muffin cup. You want to pour in enough egg mixture so each muffin cup is just about full, but leaving room so you can still transfer the pan to the oven without spilling. Depending on the how accurate I measure the vegetable filling and the exact size of the eggs I use, sometimes I have about 2 tablespoons leftover egg mixture.
Bake in the preheated oven for 20-25 minutes, until the tops are golden and the muffin tin eggs are puffy and cooked through.
Enjoy immediately, or allow to cool then store in an airtight container in the refrigerator. To freeze, freeze each egg muffin individually on a tray, then transfer them to a freezer bag.