Preheat the oven to 375°F (190°C). Line or grease a 12-cup muffin tin.
In a bowl, whisk together the flour, baking powder, baking soda, salt, and black pepper.
In another bowl, beat the eggs with milk, yogurt, and oil until smooth.
Pour the wet ingredients into the dry mixture and stir until just combined.
Fold in the diced ham, shredded cheese, and chopped green onions.
Spoon the batter evenly into the muffin cups, filling them about 3/4 full.
Bake for 18–22 minutes or until a toothpick inserted in the center comes out clean.
Let cool slightly before serving warm.