Preheat and Prepare: Begin by setting your oven to preheat at 375°F (190°C) to get it ready for baking. Lightly coat your muffin tin with oil or line each cup with paper liners for easy removal.
Mix Wet Ingredients: In a large bowl, whisk together the pumpkin puree, unsweetened apple sauce, eggs (or flax eggs), melted coconut oil, honey (or maple syrup), and vanilla extract.
Combine Dry Ingredients: In another bowl, mix the whole wheat flour, protein powder, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger.
Mix Together: Gradually add the dry ingredients to the wet mixture, stirring gently until just combined. Do not overmix; a few lumps are fine.
Optional Add-In: If using, fold in the chopped walnuts or pecans evenly throughout the batter.
Fill the Muffin Tin: Spoon the batter into the prepared muffin cups, filling each about 2/3 full to allow room for rising.
Bake: Place the muffin tin in the preheated oven and bake for about 18 to 20 minutes. Check doneness by inserting a toothpick into the center of a muffin; it should come out clean or with a few moist crumbs.
Cool and Serve: Once baked, allow the muffins to rest in the tin for about 5 minutes. Then, transfer them to a wire rack and let them cool completely before enjoying. Enjoy them warm or at room temperature.