Preheat oven to 425°F. Line 12 muffin tins with cupcake liners. You can also just spray the muffin tins with cooking spray.
In a large bowl, whisk together the flour, flax seeds, baking soda, cinnamon, ginger, salt and nutmeg.
In a medium bowl, whisk together the eggs, vegetable oil, applesauce, orange juice, brown sugar, maple syrup, vanilla extract and orange zest. Now add the carrots and apple and mix until combined.
Pour the wet ingredients into the dry ingredients and stir a few times. Fold in the raisins and pecans and mix until just combined. Be careful not to over mix.
Spoon the batter into the muffin tins all the way to the top. Bake for 5 minutes before reducing temperature to 350°F. Bake for an additional 18 minutes or until a toothpick inserted into the center comes out clean. Let cool slightly before transferring to cooling rack.
Notes
Grate your own carrots. Pre-shredded carrots are much drier and will alter the moisture level.
Don't skip out on roasting the pecans if using. By roasting them they will stay crispy in the batter and bring out the flavor.
Use an ice cream scoop to get an even amount of batter in each muffin tin.
The initial high temperature helps the muffins rise taller. If you don't care about tall muffins, just bake at 350°F.
Just like with any regular muffin that you make, you’ll know they are done when a toothpick comes out clean.