Preheat oven to 350°F. Spray mini muffin pans with cooking spray (or line them with liners).
Whisk the flour, baking powder, salt, and cocoa in a bowl to combine.
Mix the melted butter and brown sugar in a large bowl. Stir in the egg, food coloring, and vanilla. Stir in the dry ingredients.
Place about 1 tablespoon of batter into each muffin cavity. Bake until the brownies are set, 8-12 minutes. The brownies should naturally fall in the centers when you take them out of the oven, but if they don’t you can press down the centers with the handle of a wooden spoon. Cool completely in the tins.
To make the filling, beat the cream cheese and butter until smooth. Gradually add in the powdered sugar and beat until smooth.
Place the filling in a pastry bag fitted with a star tip (or a 1M tip). Remove the brownies from the tins and pipe the filling into the cups. Store the brownies in an airtight container in the refrigerator.