Preheat oven to 375 degrees and place about 16 cupcake liners into muffin tins.
In a large bowl, combine flour, cocoa powder, chocolate protein powder, brown sugar, baking soda, and baking powder.
In a seperate large bowl, whisk together the vanilla yogurt, eggs, milk, and vanilla.
Using a spatula, fold the wet ingredients into the dry ingredients and only stir until the dry ingredients disappear and are incorporated into the batter. It is important to mix this by hand to prevent from overmixing. If your batter looks dry, add more milk (one tablespoon at a time) until it reaches the consistency of muffin batter. Gently fold in chocolate chips until evenly dispersed. Scoop about 3 tablespoons of batter into each muffin tin and gently tap the muffin tin on the counter to smooth out the tops of the batter.
Bake at 375 degrees for 16-20 minutes or until fork comes out clean. Overbaking can result in dry & hard muffins, so watch the oven closely around the 15 minute mark !
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Makes 16 muffins