Preheat oven to 350°F. Place cupcake liners into muffin pan. Grate carrot.
Stir together honey, oil, pineapple, and carrot. Add eggs and vanilla and stir until well combined.
In a separate bowl, combine flours, baking powder, baking soda, cinnamon, and salt.
Add dry ingredients to wet mixture and stir just until combined.
Spoon into prepared muffin tin, filling a little more than 3/4 full.
Bake for 20-25 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Cool in pan for 5-10 minutes, then remove to a rack to finish cooling.