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Combine the flour, baking powder, baking soda, salt, and nutmeg in a bowl and stir to combine.
Mix the eggs, yogurt, sugar, melted butter, and vanilla in another large bowl.
Add dry ingredients to the wet ingredients and mix until just combined (don't over mix - the batter should be a bit lumpy - not smooth).
Carefully fold the chocolate chips or blueberries into the muffin batter.
Grease a mini muffin tray.
Divide the batter between the muffin cups and bake for 12-15 minutes at 380, or until a toothpick inserted into a muffin comes out clean.
Allow the muffins to cool for 2-3 minutes before removing them from the pan.
Place the muffins on a wire rack and allow them to cool for an additional 10 minutes.
Store the muffins in a covered container for 5-7 days.