Preheat the oven to 375° Fahrenheit and lightly spray a 12-cup muffin tin with non-stick cooking spray.
In a bowl, toss together the diced apples and 3 teaspoons all-purpose flour. Set aside.
In a big mixing bowl, whisk together the 1 cup all-purpose flour, whole wheat flour, ground cinnamon, baking soda, baking powder, white sugar, and sea salt.
In a separate medium-sized bowl, use a hand-held mixer to beat together the eggs, vegetable oil, applesauce, and vanilla extract.
Add the wet mixture to the dry mixture and mix just until it comes together. Fold in the diced apples.
Spoon the muffin mixture evenly into the prepared muffin tin.
In a small bowl, mix together the granulated sugar and ground cinnamon for the topping.
Sprinkle the topping over the muffin batter and bake for 20-25 minutes or until a toothpick or knife inserted in the center of a muffin comes out clean with just a few moist crumbs.
Cool the muffins in the tin for 5 minutes before removing.