Preheat oven to 350 F. Line a 12 cup muffin pan with liners. In a large bowl, whisk together flour, sugar, cocoa powder, salt, and baking powder.
Add in eggs, milk, vegetable oil, and vanilla extract, whisk until smooth. Evenly divide cupcake batter between the liners. Bake for 18-22 minutes. Let cool completely.
For the cookie dough, place flour and cocoa powder in a microwave-safe bowl, heat in the microwave for 40 seconds. Set aside. In a large bowl, with a mixer, beat softened butter with both sugars until fluffy. Add in milk and vanilla extract, beat until smooth. Add in flour and cocoa powder mixture, beat until combined. Fold in chocolate chips.
For the frosting, beat softened butter with powdered sugar, cocoa powder, milk, and vanilla extract, beat until smooth. Cut out the centers of each cupcake. Fill with the cookie dough. Place the tops back onto the cupcakes. Pipe frosting onto each cupcake.
