In a small bowl, microwave the flour for 1–2 minutes to heat-treat it (to make it safe to eat raw). Let it cool.
In a medium bowl, cream the butter and brown sugar together until light and fluffy. Add the milk and vanilla extract. Mix in the cooled flour until a soft dough forms. Fold in the chocolate chips.
Roll the dough into 12 small balls and place them in the freezer while you prepare the cupcakes.
Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners.
In a bowl, whisk together the flour, baking powder, and salt.
In another bowl, cream the butter and sugar until light and fluffy. Add eggs one at a time, beating well after each. Stir in the vanilla.
Add the dry ingredients alternately with the milk, beginning and ending with the dry. Mix until just combined.
Fill each cupcake liner about two-thirds full. Place a frozen cookie dough ball into the center of each batter-filled liner, pressing it down gently.
Bake for 18–20 minutes, or until the cupcakes are golden and a toothpick inserted off-center comes out clean. Cool completely.
Cream the butter and brown sugar until fluffy. Add vanilla, then gradually mix in powdered sugar.
Add milk one tablespoon at a time until the desired consistency is reached. Fold in the mini chocolate chips.
Frost the cooled cupcakes using a piping bag or spread with a spatula.