In a medium bowl, combine the flour, baking soda, and baking powder and stir to combine.
In the bowl of a stand mixer with the paddle attachment, combine the butter, light brown and granulated sugar until light and fluffy, around 5 minutes.
Add the miso paste and peanut butter to the butter mixture and mix until just incorporated. Add the egg and vanilla extract and mix until just incorporated.
Add 1/3 of the flour mixture to the bowl of the stand mixer and mix on low speed until flour mixture is just incorporated. Repeat with the remaining flour mixture in two batches until just combined.
Place the bowl of the stand mixer in the fridge to chill for 5 minutes
While the bowl is in the fridge, combine the granulated sugar and cinnamon in a small bowl and mix to combine.
Scoop one heaping tablespoon of dough and roll into a ball with your hands. Drop the ball into the bowl with the sugar and cinnamon mixture and turn to coat evenly. Place the dough on a parchment lined baking sheet or in a clean large bowl. Repeat with the rest of the dough
Chill the dough for at least two hours and up to overnight. The longer it chills, the more mellow the miso flavor.
Preheat the oven to 350 degrees Fahrenheit.
Place the dough on a parchment lined baking tray if dough was stored in a bowl. Leave several inches between dough balls.
Bake for 15 minutes of until crisp at the edge and puffy in the middle. Take tray out of the oven and bang it down on the counter. Place back in the oven to bake for another 3 minutes.
When cookies are firm at the edges and puffy in the middle again, take tray out of the oven and bang it down on the counter. This will make the cookies appear flat and crinkly in the middle.
Let the cookies cool on the baking tray for a few minutes and then transfer to a wire cooling rack. Store in an airtight container for up to 3 days.