Melt chocolates and butter in a medium bowl in the microwave for 1 minute. Stir until well-combined and smooth. Reheat in 10 second increments if needed.
Whisk in sugar and vanilla.
Whisk in eggs, one at a time.
Add dry ingredients, whisk until just incorporated.
Scoop batter into prepared muffin tin. Lightly butter your fingertips and lightly press to form a crust, causing the sides to be higher than the center of the brownie dough.
For the chocolate chip cookie layer:
Cream butter then add sugars and mix until light and fluffy.
Add eggs and vanilla.
Mix until well-combined.
Add flour, sea salt, and baking soda to butter mixture.
Mix well and then stir in chocolate chips.
Scoop chocolate chip cookie dough into the center of the brownie crust.
Baking instructions
Place muffin tin in preheated oven on the middle rack of the oven. Bake for about 25 minutes or until toothpick inserted comes out with just a few crumbs.
Remove from the oven and allow to cool for about 3 minutes.
Run a knife alongside the edge of each muffin tin to assist in the release and then invert the muffin tin on top of a parchment lined wire rack.
For the peanut butter cup layer:
While the brownies are still warm to the touch, turn back right side up and place a large peanut butter cup on top of each brownie.