In a medium bowl, stir together flour, cocoa powder, and baking soda. Set aside.
In a large mixing bowl, beat together butter, the ½ cup granulated sugar, brown sugar and the ¼ cup peanut butter with an electric mixer until combined. Add egg, milk, and vanilla; beat well. Beat in as much of the dry ingredients as you can with mixer (as the mixture will be very thick). Stir in remaining dry ingredients by hand. Form chocolate dough into 32 balls about 1 ¼ inches in diameter. Set aside.
In a medium mixing bowl, combine powdered sugar and remaining ½ cup peanut butter until smooth. Shape into 32 (¾-inch) balls.
Preheat oven to 350° F. Slightly flatten a chocolate dough ball with the palm of your hand, and top with a peanut butter ball. Shape the chocolate dough over the peanut butter filling, completely covering the filling. Roll dough into a ball. Repeat with the remaining chocolate dough and peanut butter filling.
Place dough balls 2-inches apart on ungreased cookie sheets or cookie sheets lined with Silpats. Flatten dough balls with the bottom of glass dipped in remaining 2 tablespoons granulated sugar.
Bake cookies in a 350° F oven for 8 minutes or until the cookies are just set and surface is slightly cracked. Let cookies stand for 1 minute. Transfer cookies to a wire rack to cool.
Notes
If your cocoa powder has lumps, take an extra moment to sift out the lumps.I find it easiest to get 32 balls out of the dough by cutting the dough in half (each piece is 16), then in half again (each piece is 8) and in half again (for 4 pieces), and twice more for 1 piece each.If the dough feels too sticky to handle, make sure that you added the correct measurements and all the ingredients. It may also have gotten too warm; If it’s too warm, chill it in the refrigerator for about 30 minutes.Let the chocolate peanut butter stuffed cookies cool completely, then transfer them to an airtight container, placing a sheet of parchment paper between the layers to prevent the cookies from sticking together. Keep them stored this way, on the counter for up to a week.For longer storage, these freeze very well. Allow them to cool completely. Then, place them on a baking sheet in a single layer and freeze. Once they’re frozen, transfer them to a freezer-safe ziptop bag for up to 3 months.When ready to eat, simply thaw them on the counter at room temperature.