Preheat oven to 375F. Spray or line a muffin tin and set aside.
In a large bowl, combine both flours, pumpkin pie spice, baking powder, baking soda, and salt. Set aside.
In a medium bowl, whisk together pumpkin, yogurt, honey, coconut oil, egg, and vanilla. Stir in carrots. Add wet ingredients to dry ingredients and stir just until moistened. Fold in chocolate chips and walnuts (if using).
Divide batter evenly among 12 muffin cups. Bake for 20 - 22 minutes, or until a wooden toothpick inserted in center of muffin comes out clean. Cool on a wire rack.