Preheat oven to 350F (180C). Grease with butter a standard muffin tin.
In a bowl whisk flour with cocoa powder, instant coffee, salt and baking soda. Set aside until ready to use.
In another bowl mix the butter with both sugars until creamy. Add egg and vanilla and mix until well incorporated.
Gradually incorporate flour mixture and chocolate chips.
Using an ice cream scoop, divide the cookie dough evenly between the 12 muffin tins.
Bake for 12-13 minutes. While still warm use a small jar to press down the center of each cookie
Cool on the muffin tins for about 10 minutes. Transfer the cookie cups to a cooling rack to cool completely.
Prepare the filling. In a large bowl mix cream cheese until smooth. Add powdered sugar and peanut butter and mix until combined.
In a separate bowl whip cream until stiff peaks form. Gradually incorporate into cream cheese mixture.
Transfer the peanut butter filling into a piping bag fitted with 1M star tip and pipe the filling into the chocolate cookie cups.
Refrigerate for at least 1 hour before serving.
Decorate with grated chocolate if desired.