Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners.
In a medium bowl, whisk together the flour, baking powder, and salt for the cupcake batter.
In a large bowl, beat the butter and sugar together until light and fluffy. Add the eggs one at a time, beating well after each addition. Mix in the vanilla extract.
Gradually add the dry ingredients to the wet ingredients, alternating with the milk, beginning and ending with the dry ingredients. Mix until just combined.
Fill the cupcake liners about ⅔ full with the batter. Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean. Allow to cool completely on a wire rack.
While the cupcakes are baking, prepare the cookie dough filling. In a medium bowl, beat the butter, brown sugar, and granulated sugar together until light and fluffy. Mix in the milk and vanilla extract. Gradually add the flour and mix until just combined. Stir in the mini chocolate chips.
Once the cupcakes are cool, use a small knife to cut a cone-shaped piece out of the center of each cupcake. Fill each hole with a spoonful of the cookie dough filling.