Preheat oven to 350 degrees Fahrenheit. Line a muffin pan with cupcake liners and set aside.
In a stand mixer fitted with the paddle attachment, cream the butter, peanut butter, and sugar together. Add the eggs and vanilla and beat until combined.
Add in the flour and baking powder and mix until combined. Once combined, slowly add in the milk. Stir in the chocolate chips by hand.
Scoop the batter into the cupcake liners, filling them about ⅔ full. I was able to get 12 cupcakes. Bake for 18-20 minutes or until lightly golden brown on top and a toothpick inserted in the center comes out clean. Allow the cupcakes to cool completely.
Cookie Dough Frosting
Add the flour to a small bowl and heat in the microwave in 10-15 second intervals, stirring between each one, until the flour reaches 165 degrees Fahrenheit on a thermometer. Set aside to cool.
Add the cream cheese, peanut butter, and butter to a large bowl and beat with a hand mixer or a stand mixer fitted with the paddle attachment until combined.
Slowly add in the powdered sugar, brown sugar, cooled flour, and vanilla, scraping down the sides and bottom of the bowl as needed. Add in the oats and mix until combines.
Stir in the M&M's and chocolate chips by hand.
Once the cupcakes have cooled, frost each of them with the frosting as desired before serving.