Preheat the oven to 350°F. Grease one 24-count mini muffin tin (or two 12-count mini muffin tins) with non stick spray and set aside.
Whisk together the flour, cocoa powder, baking soda and salt and set aside.
In a large bowl with a stand mixer or electric mixer, beat the butter and sugars together until light and fluffy, 2-3 minutes. Add the egg, milk and vanilla and beat until combined.
Turn the mixer on low speed and slowly add the dry ingredients until combined and the dough starts to pull away from the sides of the bowl. It will be slightly wet and sticky.
Use a heaping teaspoon to shape the dough in one-inch balls and place in each mini muffin cup. The dough will be a little wet and may stick to your fingers and hands as you're rolling. You can put a little cocoa powder on your fingers and hands to prevent this.
Bake the dough in the preheated oven for 7-9 minutes or until the cookies puff up and set. The cookies are small, so be careful not to over bake them.
Remove the cookies from the oven and immediately use the back of a teaspoon to press a whole into the center of each cookie, deep enough to hold a 1-inch peanut butter ball.
Allow them to cool slightly in the pan then carefully transfer them to a wire rack to cool completely.
While they’re cooling make the peanut butter filling. Use a stand mixer or electric mixer to cream the butter and peanut butter on high speed until smooth. Some butter lumps are okay. With the mixer running on low speed, slowly add the powdered sugar and vanilla and mix until combined.
Use a scant Tablespoon to scoop and roll the peanut butter into a small ball. Place each peanut butter ball inside the chocolate cookie.
To make the ganache, place a piece of parchment paper under the cooling rack with the cookies to catch any extra chocolate ganache that drips off. Mix all of the chocolate topping ingredients in a medium bowl. Working quickly, use a spoon to partially cover the tops of the cookies with ganache, letting it run down the sides. Allow them to set and harden before serving.