In a large bowl sift together the flour, baking powder, salt and cocoa powder and set aside. In the bowl of a stand mixer fitted with a paddle attachment cream the butter and the sugar until creamy, about 2 minutes. Add the eggs one at a time, beating well after each addition. Add the vanilla and peanut butter and continue to beat to combine.

On the lowest speed alternate adding the dry ingredients and the milk, beating until the ingredients are just combined. Use a wooden spoon to stir in the peanut butter chips.

Scoop the batter into the prepared cups, filling until 2/3 full. Bake until the tops are puffed and cooked completely through, about 25 minutes. Let cool for about 5 minutes then remove the cupcakes to a wire cooling rack until completely cooled.

In a medium saucepan over medium-low heat, stir together the chocolate chips, cream, butter and sugar. Cook, whisking occasionally, until the mixture is smooth and the chocolate has melted, about 5 minutes. Whisk in the food coloring until completely combined. Remove from heat and let cool. Once cool use a spoon to spread the ganache on the cupcakes.

Using the double boiler method to heat chocolate, bring a medium saucepan of water to a boil then place a medium heatproof mixing bowl over the top. Add the chocolate and canola oil stirring until the chocolate is smooth and completely melted. Add the food coloring, stirring to combine.

Add the halved peanut butter cups to a wire rack placed over a baking sheet. Spoon the chocolate over the top of the peanut butter cups so they are entirely covered on all sides. Refrigerate until the chocolate is hardened, about 30 minutes to 1 hour.

Attach the chocolate covered peanut butter cups to the cupcakes using toothpicks. Add the cream cheese frosting to a piping bag fitted with a small round tip. Squeeze the bag and use a knife to cut ¼” pieces of the frosting to make eyes. Dip a toothpick in the food coloring to make the blacks of the eyes. Repeat with all the cupcakes.