Preheat oven to 375°F. Prepare a 12-cup muffin pan by spraying tin with non-stick baking spray or paper liners sprayed with non-stick baking spray. Set aside.
In a large bowl, stir together pumpkin puree, eggs, oil, applesauce, almond milk and vanilla extract. Add the granulated sugar and brown sugar. Stir until smooth and well combined.
In a medium bowl, whisk together both flours, salt, baking soda, pumpkin pie spice and cinnamon.
Add the dry ingredients to the wet ingredients in two additions, mixing after each addition just until evenly moistened. Set aside.
For the Pumpkin Filling:
In a small bowl, whisk together pumpkin puree, brown sugar, applesauce, salt and pumpkin pie spice.
To Assemble for Baking:
Fill muffin cups half way with muffin batter. Dollop a small amount of filling on top, making sure it doesn't touch the sides. Evenly divide remaining batter among muffin cups. Create a little divot in the top of each muffin using the back of a 1 teaspoon measuring spoon and fill the divots with remaining filling.
Bake in preheated oven for 18-20 minutes or until a toothpick inserted in center of muffin comes out clean. Remove from oven and cool completely on wire rack.