Preheat the Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it with cooking spray.
Mix Wet Ingredients: In a large bowl, combine the pumpkin puree, Greek yogurt, honey (or maple syrup), eggs, and vanilla extract. Mix until well combined.
Combine Dry Ingredients: In another bowl, whisk together the whole wheat flour, baking soda, baking powder, cinnamon, nutmeg, and salt.
Combine Mixtures: Gradually add the dry ingredients to the wet mixture, stirring until just combined. If desired, fold in walnuts or chocolate chips.
Fill Muffin Tin: Divide the batter evenly among the muffin cups, filling each about 2/3 full.
Bake: Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Cool: Allow the muffins to cool in the pan for a few minutes before transferring them to a wire rack to cool completely.