Preheat oven to 350°.
Spray 14 regular-sized muffin cups with cooking spray.
Set aside.
In a small saucepan, melt butter, 1 cup semi-sweet chocolate chips and cocoa over low heat.
Stir mixture until smooth.
Remove saucepan from heat and whisk in granulated sugar.
Add eggs, one at a time, whisking after each addition to combine the eggs well.
Whisk in vanilla and salt.
Fold in flour with a rubber spatula or wooden spoon until well-combined.
Stir in the remaining chocolate chips and one cup of peanut butter chips.
Fill each muffin cup nearly full with the brownie batter.
Sprinkle about 10-12 peanut butter chips over top of each muffin cup.
Bake approximately 20-25 minutes at 350° until a toothpick inserted in center comes out clean and the brownie is set and edges are slightly puffed.
Cool in pan 15 minutes before removing the muffin cups to a wire cooling rack to cool completely.
Store in an air-tight container up to 3 days before refrigerating or freezing.