Start by preheating your oven to 350ºF (175ºC) and lining your baking sheets with parchment paper for easy cookie removal later.
Whisk the dry ingredients including flour, baking soda, baking powder, and salt in a medium bowl to ensure your cookies have a uniform texture.
Melt the butter in a large microwave-safe bowl, then vigorously mix in the peanut butter until smooth. Blend in both sugars, then add the eggs and yolk one at a time, followed by the vanilla, mixing well after each addition.
Gradually incorporate the dry ingredients into the wet mixture until just combined, then fold in the chocolate chips. If the dough is too crumbly, consider adding a touch of milk to reach the desired consistency.
For even more flavor, if you have time, cover and refrigerate the dough for 24-72 hours before baking. Allow it to soften at room temperature before scooping.
Scoop the dough into 3-tablespoon sized balls onto the prepared baking sheets, flattening them slightly. Add a few extra chocolate chips on top for a bakery-style look.
Bake the cookies for 12 minutes until golden. Let them cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.
Keep your cookies fresh by storing them in an airtight container at room temperature for up to 3 days.