1. Preheat oven to 350 degrees. Lightly oil or coat 24 mini muffin cups with nonstick cooking spray and set aside.
2. Whisk together the all-purpose flour, whole wheat flour, ground flaxseed, baking powder, cinnamon, and salt in a large bowl.
3. In a separate bowl, whisk the pumpkin, eggs, brown sugar, oil, milk, and vanilla until well combined. Pour the liquid ingredients over the dry ingredients and stir until just combined. Stir in the chocolate chips.
4. Spoon the batter into the prepared muffin cups. Bake 15 to 18 minutes, or until a toothpick inserted in the center comes out clean. transfer the pan to a wire rack and cool 5 minutes. Remove the muffins and cool an additional 5 minutes before serving. When making 12 full-size muffins, bake for 20-23 minutes.