Preheat oven to 350° F
Line a 12 count muffin pan with cupcake liners or spray with nonstick spray. This recipe makes 14-16 muffins.
Whisk the flour, baking soda, cinnamon, ginger, salt and flax together in a large bowl.
In a medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce and vanilla until combined. Whisk in the carrots and apples. Pour all into dry ingredients. Stir until just combined.
Spoon the batter into the cupcake liners filling them to the top.
Bake for about 25 min. Allow the muffins to cool for 10 minutes in the muffin sheet then transfer to to a wire rack to cool completely.
Cover leftover muffins and store at room temperature for 2 days or in the refrigerator for 1 week.