Preheat the oven to 350 F. Line a 12 cup muffin pan with paper liners. In a large bowl, whisk together flour, sugar, cocoa powder, salt, and baking soda. Add in eggs, melted butter, and vanilla extract, and mix until smooth.
In a medium bowl, whisk together flour, salt, and baking soda. In a large bowl, combine butter with peanut butter, granulated sugar, and brown sugar until fluffy. Add in egg and vanilla extract, and mix until smooth.
Add in the flour mixture, and mix until it is fully combined. Evenly divide the brownie batter between the lined muffin pan. Top evenly with the peanut butter cookie dough. Bake for 15-20 minutes.
