Preheat the oven to 375°F (190°C). Line a standard 12-cup muffin pan with liners or a light spray of cooking spray.
Whisk together both flours, brown sugar, baking powder, baking soda, salt, and spices in a large mixing bowl until well combined. Set aside.
In another bowl, beat the eggs lightly. Add the applesauce, vegetable oil, honey, pineapple juice, orange zest, and vanilla. Mix until well combined.
Sift the dry ingredient mixture into the wet ingredients then stir until just combined. The batter should be slightly lumpy. Do not over-mix.
Gently fold in the grated fruits and vegetables, coconut, chopped nuts, cranberries, and seeds.
Divide the batter equally among the prepared muffin cups, filling each cup no more than 2/3 full.
Bake for 10 minutes, and then reduce the temperature to 350°F. Bake for an additional 10-15 minutes. The muffins will be golden brown, and a toothpick inserted into the center will come out clean when they are done.
Allow the muffins to cool in the pan on a wire rack for about 10 minutes before transferring them from the pan directly to a wire rack to cool completely. Serve the muffins warm, room temperature, or chilled!
Notes
Store in an airtight container at room temperature up to 3 days or in the freezer up to 3 months.