Make flax egg by whisking together ground flaxseed and water. Set aside for about 5 minutes to gel up.
Preheat oven to 350°F and line a 9X5 loaf pan with parchment paper (or grease with oil).
Stir together flours, cinnamon, baking powder, baking soda, salt and nutmeg in a medium mixing bowl.
Combine applesauce, coconut sugar, coconut oil, milk, flax egg and vanilla in another mixing bowl.
Stir the dry ingredients into the wet until just combined.
Gently stir in the apple chunks.
Stir together chopped pecans, coconut sugar and cinnamon in a small bowl to make the topping.
Pour batter into the prepared loaf pan and top with crumb topping.
Place in preheated oven and bake for 45-50 minutes, or until a cake tester or toothpick come out clean.
Let loaf cool on a wire rack before attempting to remove the loaf from the pan.
Once cool, make glaze by stirring together powdered sugar and milk. Drizzle glaze over bread and serve.
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Notes
If needed, you can sub the whole wheat pastry flour for regular whole wheat flour or you can use just one type of flour.
To make this gluten-free, I recommend using a gluten-free 1:1 baking flour. I tested it with Bob's Red Mill. The bread doesn't rise as much but still tastes great!
If you don't need this bread to be vegan you can swap the flax egg for 1 regular egg.
You can sub the pecans for another nut like walnuts or almonds. I haven't tested this, but I bet you could sub the nuts for oats to make the topping nut-free.