Preheat the oven to 425°F and line a muffin tin with liners and spray with nonstick spray. Set aside.
In a large mixing bowl, combine the gluten free flour, baking soda, ground cinnamon, salt and flax seed (optional). In a separate medium bowl, whisk together the eggs, coconut sugar, honey, melted coconut oil, almond milk, vanilla, carrots and apple.
Add the wet ingredients to the dry ingredients and fold together until just combined and all the pockets of flour are gone. Add the raisins and stir until just combined, being careful not to overmix.
Divide the batter evenly between the muffin cups all the way to the top. Bake the muffins in the preheated oven for 5 minutes then, with the muffins still in the oven, reduce the heat to 350°F and bake for another 17-19 minutes or until a toothpick inserted in the center comes out clean.
Cool in the muffin tins for 5-10 minutes then transfer to a wire rack to cool completely.
