Preheat the oven to 350°F. Spray a muffin tin with nonstick cooking or baking spray or line with baking cups.
In a large bowl, mix together the milk and vinegar. Set aside to “sour”.
In a separate bowl, whisk together the flours, sugar, cocoa powder, baking powder, baking soda and salt.
Add the melted butter, eggs and vanilla to the “soured” milk, and whisk together with a fork.
Pour the milk mixture into flour mixture and mix until fully incorporated. Fold in most of chocolate chips, reserving a few to sprinkle on top as decoration.
Scoop the muffin batter into the prepared muffin tin and sprinkle with the remaining chocolate chips.
Bake for 16-20 minutes or until a toothpick inserted into the center of the muffin comes out clean. Remove from the oven and allow to cool slightly before removing to place on wire racks to cool completely.