Step 1: Preheat your oven to 350°F (175°C) and line two large baking sheets with parchment paper.
Step 2: In a medium bowl, whisk together the flour, baking soda, and baking powder. Set aside.
Step 3: In a large bowl or stand mixer, beat the softened butter, peanut butter, miso, granulated sugar, and brown sugar on medium-high speed until light and fluffy, about 3 minutes.
Step 4: Add the egg and vanilla extract to the butter mixture and beat until well combined, scraping down the sides of the bowl as needed.
Step 5: Gradually add the dry ingredients to the wet ingredients, mixing on low speed just until no streaks of flour remain. Do not overmix.
Step 6: Chill the dough in the refrigerator for at least 30 minutes to firm up.
Step 7: Scoop rounded tablespoons of dough and place them 2 inches apart on the prepared baking sheets. Use a fork to create a criss-cross pattern if desired.
Step 8: Bake for 10-12 minutes, or until the edges are golden brown but the centers still look slightly soft.
Step 9: Let the cookies cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.