In a medium bowl, whisk together the all-purpose flour, baking soda, baking powder, and salt until well combined.

Using a stand mixer fitted with a paddle attachment, cream the softened butter, brown sugar, and granulated sugar on medium-high speed for 3 minutes until light and aerated.

Add the peanut butter to the creamed mixture and beat for 1 minute until smooth and fully incorporated.

Reduce mixer speed to low and add the egg, egg yolk, and vanilla extract, mixing until just combined; scrape down the sides of the bowl as needed.

Gradually add the dry ingredient mixture to the wet ingredients, mixing on the lowest speed only until no flour streaks remain.

Cover the bowl with plastic wrap and refrigerate the dough for at least 30 to 60 minutes to solidify the fats and prevent excessive spreading.

Preheat the oven to 350°F (177°C) and line two large baking sheets with parchment paper or silicone mats.

Using a 2-tablespoon cookie scoop, portion the chilled dough into balls (approximately 40g each) and place them 2 inches apart on the prepared sheets.

Using a fork dipped in sugar or water, gently press a criss-cross pattern into the top of each dough ball to flatten slightly to about 3/4-inch thickness.

Bake for 9-11 minutes, or until the edges are just set and lightly golden, while the centers still appear slightly soft and underbaked.

Remove from the oven and allow the cookies to rest on the baking sheet for 10 minutes to finish setting before transferring to a wire rack to cool completely.