Make the crumb topping by whisking together brown sugar, cinnamon powder and flour in a bowl.
Add melted butter to it and mix till mixture resemble crumbs. Set aside.
Spray a 12 count muffin pan with non-stick spray and set aside.
Peel and chop the apples into small cubes. Set aside.
In a bowl whisk together both the flours, both the sugars, cinnamon powder, nutmeg powder, baking powder and baking soda.
In another bowl, whisk together melted butter and unsweetened apple sauce. Mix till well combined.
Add vanilla extract and eggs and mix till well combined.
Add wet ingredients to the dry and mix till combined.
Do not over-mix the batter, few pockets of flour is totally fine. The batter will be very thick.
Fold in the chopped apples and pecans.
Transfer batter to the prepared muffin pan and fill the 12 muffins pans with the batter all the way to the top.
Sprinkle the crumb topping evenly on top of the muffins.
Bake the muffins at 425 F degrees for 5 minutes and then reduce the temperature to 350 F degrees (with the muffins inside the oven) and bake for additional 15-17 minutes or till a toothpick inserted in the center comes out clean.
Transfer the muffins on to a wire rack to cool completely.