Preheat oven to 350 degrees. Line a 12-cup muffin tin with paper liners. Set aside.
In a small bowl, whisk together both flours and set aside.
In a large bowl with a hand mixer or in the bowl of an electric mixer fitted with the paddle attachment, cream butter until smooth and creamy, about 1-2 minutes.
Gradually add sugar, beating until fluffy, about 2-3 minutes.
Add eggs, one at a time, beating about 30 seconds between each addition.
Add half of the flour mixture, mix, then add vanilla extract and half of the milk. Once combined, add the remaining flours, mix, then the remaining milk. Beat just until ingredients are incorporated, but do not overmix.
Using a large spatula, gently fold in mini chocolate chips until evenly dispersed.
Divide batter evenly among liners with a scoop or spoon. The batter should fill approximately three quarters of each tin.
Bake 20 to 25 minutes or until a toothpick or cake tester inserted in the center comes out clean.
Carefully transfer the pan from the oven to a wire rack. Cool 10 minutes then transfer the cupcakes to the wire rack to cool completely.