Preheat oven to 350⁰F.
Coat mini-muffin pan (24-cup or two 12-cup) with nonstick spray.
Whisk flour, baking powder, baking soda, salt, and nutmeg in a bowl. In a separate bowl, combine yogurt, minced lemon, milk, and vanilla.
In another bowl, cream butter and sugar until light and fluffy. Add egg and beat well. Add half of flour mixture; beat until just combined. Add yogurt mixture; beat until just combined. Add remaining flour mixture and beat until combined (don’t worry if there are a few lumps.)
Fill cups of prepared muffin pan to about ¾ full. Bake until a toothpick inserted in the center of a muffin comes clean, about 15-16 minutes.
Cool for 5 minutes on a wire rack. Turn muffins out onto the wire rack.
While the muffins bake, chop the lime zest into even smaller bits. Place in a bowl with the sugar and stir until well combined. Brush the tops of the muffins with the melted butter. Roll the still warm muffins in the lime sugar to coat.