Preheat oven to 350 degrees F.
Line a baking sheet or two with parchment paper.
Using a mixer, cream butter and sugars together on low speed until the two are mostly incorporated. Increase speed to medium-high and beat butter and sugar for 1-2 minutes, or until mixture is smooth and has lightened in color and increased in volume. For best results, scrape down the sides and bottom of the bowl with a spatula at least once or twice before the creaming process is complete.
Add in egg and egg yolk, one at a time, mixing until each is fully incorporated into batter.
Add in vanilla extract and mix.
In a separate bowl, combine flours, unsweetened cocoa powder, baking soda, baking powder and salt using whisk until very well combined
Add dry mixture to wet mixture, mixing until combined, then fold in the peanut butter and chocolate chips.
Using a large cookie scoop, (1/4 cup), scoop cookie dough onto baking sheet. Also can use a smaller scoop, just scoop one scoop on top of the other to get soft, thick fudgy cookies, like a double scoop of dough. Place some extra peanut butter and chocolate chips in between each scoop and some on top if desired if you really want to burst the flavors out!
Space dough at least 2" apart - 6 per cookie sheet
Bake for approximately 12 -14 minutes. I like to do 12 minutes.
Cookies should be starting to firm up but still soft in the middle.
Remove from oven and let set on cookie tray for a couple of minutes and then allow them to cool on a wire rack.
Allow to cool completely prior to storing.