Preheat the Oven: Preheat to 400°F (200°C). Line a muffin tin with paper liners.
Mix Dry Ingredients: In a large bowl, whisk together flour, baking soda, cinnamon, ginger, nutmeg, and salt.
Prepare Wet Ingredients: In a medium bowl, whisk together eggs, oil, vanilla, and brown sugar. Stir in carrots and apples.
Combine Wet and Dry Ingredients: Gradually add the wet ingredients to the dry, mixing until just combined.
Add Mix-ins: Fold in raisins, walnuts, and coconut flakes.
Fill Muffin Tins: Spoon batter into lined muffin tin, filling each liner to the top.
Bake: Bake at 400°F for 10 minutes, reduce heat to 350°F (175°C), and bake for another 10-12 minutes.
Cool and Serve: Cool in the pan for a few minutes, then transfer to a wire rack to cool completely.