In a medium-sized mixing bowl or bowl of a stand mixer, mix together flour, baking powder, baking soda, and salt.
Mix in honey.
Add butter and mix until fully combined.
In a small mixing bowl, whisk together eggs, yogurt, and vanilla extract until smooth.
Add the egg mixture to the flour mixture and beat on medium speed until just combined.
Slowly add milk and mix on low speed until just combined.
Fill cupcake liners 3/4 full.
Bake for 14 minutes and then test to see if they are done. They are done when a toothpick comes out without wet batter stuck to it. If not done, retest every two minutes.
When the cupcakes are done, remove them immediately from the tins and leave them on a cooling rack (or just on your counter if you don't own a cooling rack) to cool.