Preheat oven to 400 degrees F (200 degrees C). Grease mini muffin cups.
Combine whole wheat flour, all-purpose flour, chocolate chips, protein powder, sugar, cocoa powder, and baking soda in a large bowl.
Whisk milk, peanut butter, eggs, oil, and yogurt in another bowl until smooth. Pour over flour mixture and stir until batter is just blended. Fill muffin cups 3/4 of the way full.
Bake in the preheated oven until a toothpick inserted into the centers comes out clean, about 10 minutes. Cool in the muffin pans for 10 minutes before removing to a wire rack until completely cooled, about 20 minutes.
