Preheat the oven to 350 degrees Fahrenheit (175 degrees Celsius) and line a 12-cup muffin tin with paper liners.

In a large mixing bowl, whisk together the whole wheat flour, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice.

In a separate medium bowl, combine the pumpkin puree, unsweetened applesauce, maple syrup, eggs, and vanilla extract. Whisk until the mixture is smooth.

Pour the wet ingredients into the dry ingredients. Stir with a spatula until just combined, being careful not to overmix the batter.

Divide the batter evenly among the 12 muffin cups, filling each approximately three-quarters full.

Bake for 18 to 22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.

Remove from the oven and allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.