Preheat oven to 350F and line baking sheets with parchment paper.
In a medium sized bowl, whisk together flour, baking soda, baking powder, and salt. Set aside.
In a large bowl, using a hand mixer (or in your stand mixer), beat together butter and sugars. Add in egg and vanilla and beat until creamy, then mix in peanut butter.
Slowly add dry ingredients to wet, continuing to mix with hand mixer. Once all of the dough is combined, stir in the peanut butter and chocolate chips.
Using a small cookie scooper, scoop into cookies and place on parchment lined baking sheet.
Bake for 13-15 minutes or until cooked through. Let cool at least 10 minutes before eating. Sprinkle with flakey sea salt if desired.