Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with cupcake liners.
In a large mixing bowl, whisk together the flour, sugar, cocoa powder, baking powder, baking soda, and salt until well combined.
In a separate bowl, beat the softened butter until creamy. Add the eggs, whole milk, and vanilla extract, mixing until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Be careful not to overmix.
Divide the batter evenly among the muffin cups, filling each about 2/3 full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean. Let the cupcakes cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
While the cupcakes cool, prepare the peanut butter frosting. In a mixing bowl, combine the creamy peanut butter, powdered sugar, and milk. Mix until smooth and fluffy. Adjust the milk to reach your desired consistency if needed.
Once the cupcakes are completely cooled, frost them generously with the peanut butter frosting.
If desired, top each cupcake with chocolate chips for a delicious garnish.