Whisk both flours, the baking powder, salt, and baking soda together in a medium bowl; set aside.
In the bowl of a stand mixer fitted with the paddle attachment, beat the butter and peanut butter together on medium speed until light and fluffy, about 2 minutes, stopping to scrape down the sides of the bowl as necessary.
Add both sugars and continue beating on medium speed until very light, about 3 to 4 minutes.
Mix in the eggs, one at a time, until well combined, then beat in the vanilla.
Reduce the mixer speed to low and gradually add the dry ingredients, mixing just until combined.
Using a rubber spatula, stir in the chocolate chips until evenly distributed.
Press plastic wrap against dough and refrigerate for at least 4 hours.
When ready to bake, preheat oven to 350 degrees F.
Divide the dough into 2½-ounce balls and place on the prepared baking sheet, leaving at least 2 inches of space between the cookies.
Bake for about 15-17 minutes, or until the edges are set and golden brown.
Transfer the baking sheet to a wire rack and allow the cookies to cool for a few minutes before removing the cookies to the rack to cool completely.
