Preheat the oven to 350ºF. Line a muffin tin with paper muffin cups and set aside.
In a large bowl, combine the applesauce, egg, honey, melted butter, and vanilla extract. Stir until fully combined.
In a small bowl, mix together the whole wheat flour, baking soda, salt, and cinnamon.
Add the flour mixture to the wet ingredients and stir until just blended. Do not overmix.
Fold in the grated carrots, orange zest, chopped pecans, drained raisins, and grated apple.
Pour in the orange juice and stir to incorporate fully.
Scoop 1/4 cup of batter into each muffin cup.
Spray a large sheet of foil with cooking spray and gently place the foil over the muffin tin.
Remove the foil for the last 5 minutes of baking time.
Bake for 22-25 minutes, until a toothpick inserted in the center of a muffin comes out clean.
Let morning glory muffins cool in the muffin tin for 2 minutes.
Transfer muffins to a cooling rack to continue cooling and enjoy.