Preheat the oven to 375℉. Lightly spray muffin pans with cooking spray and set aside.
In a large bowl, mix together the flours, oats, baking powder, baking soda, salt and brown sugar.
In a separate bowl, mix together the maple syrup, peanut butter, Greek yogurt, egg, vanilla and milk until fully combined.
Slowly mix the wet ingredients into the dry ingredients until just combined. Fold in the chocolate chips.
Divide the batter evenly into 16 muffin cavities and bake in the preheated oven for 15-20 minutes, or until a toothpick inserted comes out clean. Allow to cool in the pan for around 5 minutes before transferring to wire racks to cool completely.