Preheat oven to 400°F. Line a 12-cup muffin tin with paper liners or coat with cooking spray.
Whisk 1 cup whole-wheat flour, 1 cup all-purpose flour, ½ cup almond flour, 1 tablespoon baking powder, 1 tablespoon pumpkin pie spice, 1 teaspoon baking soda and ¼ teaspoon salt in a medium bowl.
In a large bowl, whisk 1¼ cups yogurt, ½ cup applesauce, 2 eggs, 6 tablespoons brown sugar and 1½ teaspoons vanilla until well combined. Add the flour mixture and stir until nearly combined. Using a rubber spatula, fold in ½ cup carrot, ½ cup apple and ¼ cup raisins just until evenly distributed.
Spoon the batter evenly into the prepared muffin tin (about ⅓ cup per muffin). Top with 2 tablespoons walnuts and 1½ tablespoons oats.
Bake for 5 minutes. Without opening the oven, reduce the temperature to 350°F and continue baking until puffed, golden and a wooden pick inserted in the center comes out clean or with moist crumbs, 14 to 16 minutes. Let cool in the pan for 5 minutes, then transfer to a wire rack. Let cool for 20 minutes before serving warm, or let cool to room temperature, about 30 more minutes. Recipe developed by Tricia Manzanero Stuedeman
