Preheat the oven to 350°F (175°C). Line the muffin tin with muffin liners or grease it lightly.
In a large mixing bowl, whisk together the whole wheat flour, baking soda, baking powder, salt, cinnamon, nutmeg, and ginger.
In another bowl, combine the pumpkin puree, applesauce, maple syrup or honey, eggs, and vanilla extract. Mix until smooth and well combined.
Gradually add the wet mixture to the dry ingredients, stirring gently with a rubber spatula until just combined. If using, fold in your choice of nuts or chocolate chips.
Divide the batter evenly among the 12 muffin cups, filling them about ⅔ full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
For a different flavor and texture, consider substituting half of the whole wheat flour with almond flour or coconut flour.
If desired, increase the maple syrup or honey by a tablespoon for added sweetness.
Store the muffins in an airtight container at room temperature for up to 3 days or freeze them for up to 3 months.