Preheat your oven to 375°F (190°C). Thoroughly grease a 12-cup muffin tin with cooking spray or line with silicone muffin cups for easier removal.
Wash and chop all vegetables to similar small dice sizes (approximately 1/4 inch pieces) to ensure even distribution and cooking. Blot excess moisture from tomatoes and spinach with a paper towel to prevent your egg cups from becoming soggy.
In a large bowl, whisk eggs and milk until fully combined and slightly frothy. Season with salt and pepper.
Fold the chopped vegetables and herbs into the egg mixture. Be gentle to maintain the air you've incorporated during whisking. Reserve about 2 tablespoons of cheese for topping.
Using a 1/4 cup measuring cup or ladle, fill each muffin cup about 3/4 full with the egg mixture. This allows room for expansion while baking. Distribute the vegetable pieces evenly among cups.
Sprinkle the reserved cheese on top of each egg cup.
Bake for 20-22 minutes until the centers are set and the tops are slightly golden. They should spring back lightly when touched.
Allow to cool for 5 minutes before removing from the tin.