Preheat the oven to 350F and grease a 24-count mini muffin pan. See the note below regarding cooking time if using a regular muffin pan.
In a large bowl, whisk eggs, plain Greek yogurt, and milk. Add ham, cheese, salt and pepper.
Distribute the egg mixture evenly into the muffin pan cups, filling them about ¾ of the way up.
Bake in the preheated oven for 15-18 minutes. Remove the pan from the oven and let them cool in the pan before carefully removing them with a small knife or small spatula.
Once cooled, refrigerate the egg muffins in an airtight container or zip bag for up to 3 days.
For lunch:
To enjoy these at room temperature, place 4 to 6 egg muffins inside the main compartment of a lunch container.
To eat warm, heat the egg muffins in the microwave for 1 minute, stopping the microwave halfway through to flip them over. Immediately transfer them inside a thermos container and close the lid.
Finish packing this lunch by adding fruit, veggies, and any other sides inside a bento box. Pack everything inside a lunch bag.
Notes
The cooking time using a mini muffin tray (yields 24) is approximately 16 to 18 minutes. Using a regular-sized muffin tray (yields 12) requires a longer baking time of approximately 26 to 28 minutes.