Line a 12-cup muffin tin with paper liners and set aside. Preheat your oven to 400°F (200°C). This ensures that your oven and pan are ready when the batter is mixed.

In a medium bowl, add the whole wheat flour, all-purpose flour, packed light brown sugar, baking powder, baking soda, pumpkin pie spice, cinnamon, and salt. Whisk these ingredients together until thoroughly combined, ensuring an even distribution of the leaveners and spices.

In a large bowl, add the pure pumpkin, unsweetened applesauce, melted coconut oil, coarsely shredded apple, vanilla extract, and grated carrots. Whisk everything together until well combined. I like to make sure the coconut oil is fully melted and slightly cooled so it blends smoothly.

Add the dry ingredient mixture (from Step 2) into the wet ingredients (from Step 3). Stir gently until just combined—be careful not to overmix, as this will help keep the muffins tender. Fold in the dried cranberries, sweetened coconut flakes, and chopped pecans until evenly distributed throughout the batter.

Divide the muffin batter evenly among the prepared muffin cups. Bake in the preheated 400°F oven for 24 to 28 minutes, or until a toothpick inserted into the center comes out clean or with just a few crumbs attached. Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely. I find that letting them rest briefly in the pan helps set their structure and makes them easier to handle.