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. The dough may be used in batches, and can be refrigerated for up to 72 hours.
When ready to bake, preheat oven to 350 degrees F. Line baking sheets with parchment paper or a silicon baking mat.
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. Repeat with remaining dough (be sure to allow the baking sheet to cool between batches or use additional baking sheets). The cookies can be stored at room temperature in an airtight container for up to 4 days.
Note: Please note that while I do provide the cup equivalents in the recipe above per reader feedback, I HIGHLY recommend weighing the ingredients for this particular recipe.Nutritional values are based on one serving