Preheat your oven to 325°F (160°C). Lightly grease a 12-cup muffin tin, preferably silicone for easy removal.
In a medium bowl, whisk together the eggs and milk until well combined and slightly frothy. Season with salt, pepper, and any optional seasonings.
Stir in the shredded cheese, cooked protein, and chopped vegetables. Mix gently until everything is evenly distributed.
Pour the egg mixture evenly into the prepared muffin cups, filling each about two-thirds full.
Bake for 20-25 minutes, or until the egg bites are set and a toothpick inserted into the center comes out clean. The tops should be lightly golden.
Let the egg bites cool in the muffin tin for a few minutes before carefully removing them. Serve warm.