Whisk together the flour, baking powder, baking soda, and salt. Set aside.
Using an electric mixer on medium speed, beat the butter, peanut butter, brown sugar, and sugar until light and fluffy. Add the eggs, one at a time, mixing well after each addition. Mix in the vanilla.
Reduce mixer speed to low. Gradually add the flour mixture, mixing just until combined.
Stir in the chocolate chips.
Divide the dough in half, placing one half in a separate mixing bowl.
Add the cocoa powder to one half of the dough, and mix just until combined.
Chill the two doughs for 1 hour.
Preheat oven to 350°F (175°C). Line baking sheets with parchment paper or silicone liners.
Using a tablespoon of each dough, form the dough into a ball* and place on the prepared pans.
Bake, one pan at a time, 12-15 minutes, or until the cookies are golden brown.
Cool the cookies on the pan on a wire rack for 10 minutes. Then transfer the cookies from the pan to a wire rack to cool completely.
Notes
*I like to use a scoop for the two doughs and then press them together a bit before forming into a ball. Feel free to get creative with your swirling techniques!