Preheat the oven to 350°F (175°C). Line 48 mini muffin cups with paper liners and set aside.
Place the 1 cup (2 sticks) butter and 6 oz bittersweet dark chocolate in a microwave-safe bowl. Microwave in 20–30 second intervals, stirring well between intervals, until the butter and chocolate are fully melted and the mixture is smooth. Set aside to cool slightly.
Stir the 2 cups granulated sugar and 5 tablespoons cocoa powder into the melted chocolate-butter mixture until evenly combined.
Add the 4 whole eggs one at a time, stirring after each egg until incorporated. Stir in 1 1/2 teaspoons vanilla.
In a separate bowl, whisk together the 1 3/4 cups all-purpose flour, 1/2 teaspoon baking powder, and 1 teaspoon salt.
Fold the dry ingredients into the chocolate mixture just until combined and no large streaks of flour remain. Do not overmix.
Using a spoon or small scoop, fill each prepared mini muffin liner about 2/3 full with batter.
Unwrap 48 Mint Truffle Hershey's Kisses. Press one unwrapped Kiss into the center of the batter in each filled mini muffin cup so it is partially embedded but still visible on top.
Bake in the preheated oven for 10–12 minutes, or until the brownie edges are set and a toothpick inserted near (not through) a Kiss comes out with a few moist crumbs (centers will be slightly fudgy). Avoid overbaking.
Remove the pan from the oven and transfer to a wire rack. Cool the brownie bites completely in the pan (about 30–60 minutes) before frosting so the frosting will not melt.
To make the frosting, place the 1/2 cup softened butter in a mixing bowl and beat until smooth. Gradually add the 2 cups powdered sugar and beat on low to incorporate, then increase speed and beat until creamy.
Add 1 teaspoon peppermint extract and 1 teaspoon vanilla to the frosting and beat until evenly mixed. Add green food coloring to tint to your desired shade. If the frosting is too thick to spread, add a splash of milk and mix until it reaches a spreadable consistency.
Once the brownie bites are completely cool, frost the top of each brownie bite with the peppermint frosting.
If desired, top each frosted brownie bite with an additional Mint Truffle Hershey's Kiss as a garnish. Serve.