Add in the protein powder, cocoa powder, flour, baking powder, and sweetener. Blend again until ingredients are combined. Pour the batter into the baking dish.
Bake for 30-35 minutes, or until the edges are set. A toothpick inserted along the edges should come out clean and inserted in the middle should come out mostly clean.
Using a hand mixer or food processor, combine the cream cheese, protein powder, almond milk, confectioners sugar, peppermint extract and food coloring.
Melt the butter and whipping cream in a microwave safe bowl in 20 second intervals, stirring in between, until butter is melted. Add in the chocolate chips, and stir until silky and smooth.
Add the chocolate ganache over the creamy mint layer. Gently spread with a knife or silicone spatula. Place the brownies in the refrigerator to set for a minimum of one hour, or until ready to eat.
These brownies are best the next day, chilled, after the texture has set and the flavors have come together overnight. Keep stored in an airtight container in the fridge.