Preheat oven to 425 degrees F. Spray a 12-count muffin pan with nonstick spray.
Whisk the flourm baking soda, cinnamon, ginger, salt and flax together in a large bowl.
In a medium bowl, whisk the eggs, brown sugar, oil, applesauce, orange zest, juice, and vanilla together until combined. Add carrots.
Pour the wet ingredients into the dry ingredients and stir to combine. Add craisins. Stir.
Spoon the batter into the prepared baking pan, fill them to the top
Add pan to the oven and bake at 425 for 5 minutes.
Keeping the muffins in the oven, reduce the temperature to 350 degrees F and bake for 18 minutes. A toothpick inserted into the center should come out clean when done.
Remove from oven and allow to cool for 10 minutes in pan. Transfer to a wire cooling rack to cool.