Preheat the oven to 350°F. Line a muffin tin with liners.
Combine dry ingredients: in a large mixing bowl, combine whole wheat flour, coconut sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger.
Combine wet ingredients: in a medium bowl, whisk together eggs, almond milk, applesauce, oil, vanilla, and grated apple.
Make a well in the dry ingredients and add the wet ingredients. Mix until the wet ingredients are incorporated. There should be no streaks of flour mixture in the batter, but it's okay to leave the lumps. Be careful not to over-mix the batter to avoid tough, chewy muffins.
Make the cobbler topping: melt the butter. Add flour, sugar, and cinnamon to the melted butter. Mix until the butter is distributed and small pebble size beads form. Set aside.
Fill the muffin liners about ¾ full with batter. Top with a generous amount of cobbler topping. Bake the muffins for 14 to 18 minutes. Transfer to a cooling rack. Enjoy! These muffins pair beautifully with apple butter.