Preheat the oven to 350 and line a 12 cavity muffin tin with liners and set aside.
In a medium mixing bowl, whisk together the melted butter, white sugar and brown sugar.
Whisk in the eggs, greek yogurt, milk and vanilla extract until smooth.
Whisk in the gluten free flour, baking powder, baking soda and salt. Mix in the chocolate chips.
Scoop out 2 1/2 cups of batter into a second bowl. Whisk in the cocoa powder and milk.
Use a spoon to alternate scooping the vanilla and chocolate batter into a muffin tin. There really isn't a right or wrong method here, you can leave more distinct sections or swirl them together a bit.
Top with extra chocolate chips and bake for 20-24 minutes or until a toothpick comes out clean.
Let cool for about 20 minutes before serving and enjoy!