Preheat oven to 425°F. Line a 12-cup muffin pan with paper liners or lightly grease with nonstick spray.
In a large bowl, whisk together the 1 cup (240g) pumpkin puree, ¾ cup (180g) plain or vanilla Greek yogurt, 2 large eggs, ¼ cup (80g) maple syrup, 3 tablespoons (42g) avocado oil or melted butter, and 1 teaspoon vanilla extract until smooth.
In a separate bowl, whisk together the 1½ cups (180g) all-purpose flour, ½ cup (50g) vanilla or unflavored protein powder*, 1 teaspoon baking powder, ¾ teaspoon baking soda, ½ teaspoon salt, 2 teaspoons cinnamon, ½ teaspoon ground ginger, ¼ teaspoon nutmeg, and ⅛ teaspoon ground cloves or allspice.
Add the dry ingredients to the wet ingredients and gently stir until just combined. Don't overmix. Fold in the optional ⅓ cup (55–60g) mini or regular chocolate chips, if using.
Divide the batter evenly among the muffin cups, filling each completely full. Sprinkle the tops with turbinado sugar, extra chocolate chips and chopped pecans, if using.
Bake at 425°F for 5 minutes, then, without opening the oven, reduce the temperature to 350°F and bake for another 12–15 minutes, or until the tops are rounded and a toothpick inserted in the center comes out mostly clean. Check at the 12 minute mark (mine were done).
Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely.