Preheat oven to 350°F Line 12-cup muffin pan with paper liners.
In a small bowl, mix together flour, cocoa powder, baking powder and salt.
In a large bowl, using electric mixer, beat together granulated and brown sugars and butter until well combined.
Add peanut butter, beating until smooth. Beat in egg and vanilla until mixture is smooth.
Alternately beat in flour mixture and milk, making three additions of flour mixture and two of milk, beating until smooth. Stir in chocolate chips.
Scoop batter into prepared muffin cups. Bake in preheated oven for 20-25 minutes or until tops of cupcakes spring back when light touched. Let cool in pan on rack for 10 minutes. Remove from pan and let cool completely on rack.