Preheat the oven to 350°F. Spray 6 wells of a standard muffin pan with cooking spray. Set the pan aside.
In a large, microwave-safe bowl, melt butter and chocolate in the microwave in 30 second increments. Whisk until smooth.
Add both sugars and whisk until combined.
Add vanilla and eggs and whisk until combined.
Add flour, cocoa powder, and salt and fold into the sugar mixture.
Spoon 3 Tablespoons of batter into each of the greased wells of the muffin pan.
Bake for about 18 minutes, until a toothpick inserted into the center of a brownie comes out with just a few moist crumbs.
Immediately after removing the brownies from the oven, use the back of a Tablespoon to press an indent into the center of each brownie. Use a thin cake tester or knife to separate the sides of the brownie cups from the pan and spin each brownie to loosen its bottom from the pan to avoid sticking. Let the brownies cool completely.
Make the peanut butter filling.
In a small bowl, add peanut butter, confectioners' sugar, and vanilla. Use a handheld electric mixer to beat the mixture on medium speed until well blended.
Scoop 1 Tablespoon of the peanut butter filling into the center of each brownie cup.
Make the chocolate ganache topping.
Place finely chopped chocolate in a heatproof bowl.
Add the cream to a small saucepan and heat just until it begins to simmer.
Pour the heated cream over the chocolate and let it sit for 2 minutes.
Stir with a rubber spatula until the chocolate is completely melted and the mixture is smooth and shiny.
Spoon 1 Tablespoon of ganache over the top of each brownie cup.
Optional: Sprinkle chopped peanuts and flaky sea salt over the ganache to garnish the brownies.
Notes
Storage: Store leftover brownies in an airtight container at room temperature for up to 2 days or in the fridge for up to 4 days.