Preheat oven to 400 degrees. Spray your muffin tin with cooking spray, or use liners if you prefer.
In a large bowl, combine both flours, baking powder, baking soda and salt.
Make a well in the center of the bowl. In the well, add eggs, yogurt, brown sugar, milk, butter and vanilla.
Mix wet ingredients in center of bowl and then slowly incorporate flour mixture until just combined.
Add chocolate chips and mix until incorporated.
Evenly divide batter into prepared muffin tins.
Bake 15-17 minutes or until a toothpick inserted in the center of the muffin comes out clean.
Let cool for a few minutes in the tin, then remove from tin and cool completely on counter or wire rack.
Store in an airtight container 3-4 days. You can also freeze up to 3 months.