Preheat the oven to 350 degrees F. Spray a 9x13-inch baking dish with nonstick spray.
For the brownies, add the butter and chocolate to a microwave-safe bowl and microwave until melted, 30 to 60 seconds. Once semi-melted, stir constantly to fully melt. Set aside to cool for 5 minutes.
In a small bowl, whisk together the flour, cocoa powder, baking soda, baking powder, and salt.
In a large bowl, whisk together the melted butter-chocolate mixture and granulated sugar. Whisk in the eggs, egg yolk, and vanilla until smooth.
Using a large spoon, mix in the dry ingredients until well combined. Stir in the chocolate chips. Pour the batter into the prepared dish.
Bake for 25 to 30 minutes until set and no longer jiggly in the middle. Remove from oven and allow to cool for 30 minutes.
For the peanut butter filling, combine melted peanut butter, powdered sugar, and coconut oil until smooth. Pour over the brownies, spreading with a spatula. Let cool completely for about 20 minutes.
For the ganache, place chocolate in a bowl. Heat heavy cream in a saucepan until it bubbles around the edges. Pour over the chocolate and let sit for 30 seconds. Stir until smooth.
Pour the ganache over the brownies and top with chopped peanut butter cups. Allow to sit for 30 minutes before cutting.
Note: The brownies will stay fresh for 2 to 3 days at room temperature, covered or in an airtight container. They can be refrigerated for a few days longer.