Preheat the oven to 425°F. Line 9 muffin cups with liners and set aside.
In a small bowl, mix the flour, baking powder, baking soda, and salt. Set aside.
In a separate bowl with a hand mixer or a stand mixer fitted with a paddle attachment, cream the butter and sugar on high until light and fluffy, about 3 minutes. Add the egg and beat for an additional minute. Add the yogurt and vanilla, and beat until everything is combined.
Slowly add the dry ingredients to the wet ingredients, mixing until the batter begins to come together but is not fully incorporated. Fold the chocolate into the batter, stirring until just combined. The batter will be thick!
Scoop the batter into the prepared muffin tins, filling them just shy of the top of the liner. Fill any empty muffin cups halfway with water. This prevents your pan from burning or warping in the oven. Sprinkle tops with granulated sugar.
Bake for 5 minutes at 425°F, then turn the oven down to 375°F and bake for an additional 15 minutes until the muffins are golden brown. Allow the muffins to cool for at least 5 minutes before eating. Enjoy!