Preheat the oven to 350°F. Lightly grease 18 cups in a regular size muffin tin and set aside.
Make the peanut butter dough. In a large bowl, or the bowl of a stand mixer, whisk together the melted butter, egg, brown sugar, granulated sugar, peanut butter, and vanilla until combined. Add the flour, baking soda, and salt and mix until just combined. Don’t over-mix. Stir in the chocolate chips.
Make the brownie dough. In the bowl of a stand mixer, or with an electric mixer, cream together the butter, sugar, brown sugar, and vanilla until light and fluffy. Add the egg and mix again until well combined. Whisk together the flour, cocoa powder, salt, and baking soda. Add the dry ingredients to the butter mixture and mix until well combined. Mix in the chocolate chips.
Divide both the peanut butter dough and the brownie dough into 18 pieces (about 1 tablespoon brownie dough and 1 1/2 tablespoons peanut butter dough for each cup - there IS more peanut butter dough, it’s okay, they’re terrific that way!) and roll each piece of dough into a ball. Press one ball of each dough into the prepared muffins cups. Bake for 9-12 minutes until the tops are just set and the edges are starting to brown; do not over-bake.
Let the brookie cups cool completely before removing them from the muffin tins. Store in an airtight container at room temperature for up to 5 days, or freeze for up to 3 months.
Notes
These brookie cups are quite large. If you’d like them to be smaller, make them in 36 mini muffin cups instead, using half the amount of dough for each cup. Reduce the baking time to 7-8 minutes if you are making the smaller version.