Preheat the oven to 400 degrees F. Coat a 12-capacity standard muffin pan with cooking spray.
In a small bowl, mix together the pecans, 2 tablespoons of the brown sugar and the cinnamon.
In a medium bowl, whisk together the all-purpose and whole wheat flour, baking soda and salt.
In a large bowl, whisk the remaining 3/4 cup sugar and the oil until combined. Add the eggs, one at a time, whisking well after each addition. Whisk in the applesauce and vanilla.
Whisk in the flour mixture in two batches, alternating with the buttermilk. Whisk just until combined. Gently stir in the apple chunks.
Pour the batter into the prepared muffin pan and sprinkle with the pecan mixture. Tap the pan on the counter a few times to remove any air bubbles. Bake until a wooden pick inserted in center of one of the muffins comes out clean, 20 to 25 minutes.
Let cool on a wire rack for 15 minutes. Run a knife around the muffins to loosen them and unmold. Cool completely on the rack.