Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease the cups.
In a large bowl, whisk together pumpkin puree, eggs, Greek yogurt, maple syrup, oil, and vanilla extract until smooth.
Add the flour, protein powder, baking powder, baking soda, pumpkin pie spice, cinnamon, and salt.
Stir gently until the ingredients are just combined. Do not overmix.
If the batter is very thick, add milk one tablespoon at a time until it reaches a thick but spoonable consistency.
Fold in chopped pecans or other optional additions.
Divide the batter evenly between the muffin cups, filling each about ¾ full.
Bake for 18–23 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Cool the muffins in the pan for 5 minutes, then transfer them to a wire rack to finish cooling.